Guns, gunpowder, and firearms have been around for quite some time. Gunpowder first showed its face in China around the 9th century, then spread to the Middle East, and Eastern Europe until finally reaching Western Europe sometime after the Crusades. Firearms have existed in some form as well, ever since China invented the hand cannon—a handheld (but heavy) gunpowder-filled tube—in 1232. And in 1364, we have the first recorded use of shooter-lit wicks by hand that ignited gunpowder that was loaded into a gun barrel - the matchlock arquebus. So guns actually had a place in the medieval world and are not a purely modern phenomenon. So why do Fantasy fiction and RPG developers treat it like a Redheaded Stepchild? In their worlds, guns don't exist. Cannons maybe, gunpowder possibly, rockets if they're having a good day... but no guns.
There are three main issues tied with this trope.
Mix and match troopers.
It's frequently attributed to the assumption that guns ended the era of knights; this isn't true. Guns and knights existed side-by-side for over 300 years. After the advent of guns blacksmiths would deliberately shoot at their armour—and customers would look for the dent, because it indicated that the armour would stop bullets. That's the origin of the term 'bullet proof' -- the armour was proofed (tested) against bullets. Early guns were not superior to traditional projectile weapons in every respect. They were more like crossbows, point-and-trigger (minimal training requirement) weapons with low rate of fire (and initially used a trigger mechanism borrowed from them). In fact, an English officer seriously suggested in the late 18th century that the Redcoats go back to the longbow, for the improved rate of fire. He was ignored, of course; he had forgotten about the training issue... although the English had still been using longbows as late as the Thirty Years' War, causing enough deforestation that one of the reasons they switched was because there was hardly a yew tree left in Europe anymore.
The real change in warfare was the Swiss introduction of pikes in the 15th and 16th centuries—much like the Greek phalanxes, but the Swiss were much more known for charging with them. They were first stopped by the fittingly-named Francis I of France, who used field fortifications—and musketeers.
Knightly charges had been showing vulnerabilities for some time before this happened, though. They were only dubiously useful in the Crusades (11th through 14th Centuries), and useless against the Mongols, as both the Mongols and the Turks used light cavalry and didn't field solid ranks of troops. Longbows had difficulty penetrating plate armor (the difficulty dependent on the bow and armor), contrary to popular belief, but Crécy and Agincourt did reveal further problems—at Crécy (1346), the French lost because their horses had no barding armor, and so had no protection against arrows, but at Agincourt (1415), they lost because they did have barding armor, and so got stuck in the mud. Yet worse were the introduction of very literal Panzerkampfwagens in the Hussite Rebellion (1415-1436) -- the Bohemians (modern Czech Republic and Slovakia) invented the wagon circle to defend against Hapsburg knights, and attacked with massed wagons carrying light cannon and ten or twelve peasants with flails. They won, by the way; moderate Hussites had religious freedom in Bohemia until the Thirty Years' War (when they got caught up in the Catholic-Protestant wars that had begun with the Smalkaldic War of 1525).
So, in short, knightly charges were dead without needing firearms to kill them. Personal firearms (including cavalry pistols) were if anything more useful in countering the new styles of heavy infantry; before long, though, the musket meant the conversion of knights into cavalry (not necessarily noble, and taking orders from the general rather than acting largely on their own), and the relegation of pikes to uselessness except in defending against cavalry attack. (The Janissaries managed to fight with musketeers without using any pikemen at all.)
Although plate armour was worn up till the middle of the 17th century, improvements that led to increased muzzle velocity and higher bullet calibre rendered it pointless to have without making it thicker and heavier, which was just not practical. That's why you see pictures of 17th century troops in metal breastplates and helmets, whilst by the 18th they'd abandoned them, though the garish colours and tricorne hats are quite spiffing. Breastplates and helmets wouldn't return until World War I, when the sheer quantity of shrapnel put out by modern artillery (plus the technique of indirect fire that allows one to deliver said shrapnel even if you can't see where the shell will land) brought both back (often based on medieval designs; compare the kettle hat to the Brodie and Adrian helmets or the sallet to the iconic Stahlhelm).
The use of mixed pikes and firearms (pike-and-shot) continued for quite a long time, but by the end of the 17th century the arrangement had more or less disappeared. The reason was the widespread adoption of an innovation that came from (according to legend) an ingenious blacksmith of Bayonne, France, who realized that a gun was basically a pike-staff that could shoot bullets. Attach a blade to the end of a gun (called a bayonet to this day), and voila! you have a serviceable spear. After some problems - like how to remove a blade that you inadvertently jammed in your gun - were ironed out, bayonets were more or less standard issue in European arsenals. They still remain in use today, though more as a utility knife and a training tool for aggression.
Never bring a gun to a sword fight.
Of course, there are also dramatic reasons for this trope.
By Heracles, this is the end of man's valour!
—King Archidamus of Sparta (IV century B.C.), according to Plutarch, cried out on seeing the missile shot by a catapult. (Thirty Years' War-era writers thought the same.)
As cool as gun fights can be, they just can't accomplish the level of intensity of a one-on-one duel with swords. If a hero has a gun, he can just shoot the villain from afar. But with swords, they can get up close and personal, engage in witty banter, look each other in the eye, and, if one gets that fatal cut or thrust in, engage in the drama of watching the other die. This is why even modern-day Action Movies will often have their final showdown be a hand to hand confrontation between the hero and the villain rather than a gun fight.
The reason may also be that guns are too modern. They're the primary weapon of choice in the real world. If fantasy authors want to achieve that escapist, ancient feel in their story, they have to use ancient weapons. Guns don't have that level of romance. This could also be the reason why Automatic Crossbows are excused despite being functionally similar to guns. There is also the widespread perception that guns take all the "skill" or "honor" out of fighting and make the heroes look cheaper: no intensive training with ancient masters, just "BANG! He's dead."
One is only left to wonder if some long time in the future, where they fight with yet-unimaginable weapons, it's going to be guns that carry the "oldie but goodie" flavor of cold steel in today's fiction.
Ready, aim... fireball!
May or may not be justified in Magitek settings. Why bother with explosives when you can blow somebody up with a fireball? Because anyone can use a gun, but not everyone can throw fireballs. This is a common issue of technology versus magic: technology works for people who haven't spent years studying the sacred mysteries. (The same problem exists for longbows.)
But if the magic trinket can be activated by anyone, why bother with explosives when you can blow somebody up with a fireball from a wand? 'Point, say the command' is just as simple as 'point, pull the trigger' assuming a wand doesn't just need a thought to activate which in itself is advantageous. With greater power and availability of magic this becomes less and less of a problem. In other words why bother with a gun that's heavy, has limited ammunition and chances of jamming when you can use a little inconspicuous stick that has limitless shots and can be used for a variety of functions aside from killing. Especially true if the setting can have small wands or similar magical trinkets capable of mass destruction. The same can't always be said of guns unless they're some kind of Magitek.
Despite all of this, there are writers who are talented enough to make guns work in their fantasy settings and even have them achieve a level of coolness equal to medieval weaponry. Perhaps it's understandable why guns aren't seen much in fantasy settings, but it's still nice (if you like guns in your fantasy) when authors manage to do it. After all, there were not only loosely historical The Three Musketeers, but Baron Munchausen himself used a firearm and it didn't made his stories any less of... what, Heroic Fantasy?
Conversely, assuming that gunpowder must automatically exist once reaching a certain level of advancement is to fall into a logical fallacy; development can happen at different rates in different fields, especially in a world that already has Functional Magic to make long-ranged destructive attacks. This is particularly the case if the functional magic and/or setting results in tactics differing greatly from the setting in which early guns found their first use in real history: firing in volleys using soldiers marching in ranks on battlefields. Guns present their own set of logistical issues in the form of supplies of gunpowder, as well as the cost of munitions (which severely curtailed the number of rounds of ammunition that gunpowder armies could use in training until the second half of the 19th century).
Or maybe the author outright despises guns and wants to create a world where they - and whatever other technologies the author may think are ruinous - do not exist for that purpose alone.
One historical note that is apt ignored was that the discovery of gunpowder was a major fluke in human history, perhaps the most major one too. Unlike many other technologies likes metalworking, stone-cutting, carpentry as well inventions like spoons, swords, wheels and bows etc. which were independently discovered all over the world gunpowder was discovered exactly once by accident by people who weren't even looking for it: The Chinese. They were in fact searching for an alchemical concoction that would grant immortality and just happened to discover something that explodes which they turned into rudimentary weapons. After which it spread to the West where Muslims and the Europeans eventually adapted them into guns and cannons.