When paintball was first played, the devices used to shoot the paintballs were almost uniformly called paintball guns (because they, for all intents and purposes, are guns - air guns). With time, though, they also began to be referred to as paintball markers.
The story behind the switch goes as follows, though much of my information is anecdotal, so take it for what it's worth.
When paintball originally started it was typically played in the woods with players dressed in camouflage who would sneak around and try to shoot each other. At some point, paintball promoters decided to distance themselves from this army-man version of the game and, with the rise of tournament speedball, an effort was made to call the devices which propel paintballs "paintball makers" which "mark" the opposing team as opposed to "guns" which "shoot" or "kill."
Following 9/11, there was a larger, industry-wide push towards the more politically correct term "paintball marker" to further distance the sport from anything having to do with violence or terrorism.
In the subsequent years, there are still those that only refer to paintball launching devices as "paintball markers," but I've noticed a trend back towards "paintball gun" in the mainstream lexicon. In just the past few years, most retailers that did refer to the equipment as "markers" have, for the most part, returned to using the term "paintball gun."
For my part, I usually refer to the equipment as a paintball gun, though I use the term marker interchangeably. While I don't mind the term "marker," I don't think that it really changes perceptions of the sport as most neophytes and non-players are simply confused by the term.