Gnomes have several things against them.
1) they're the only one of the standard PC races that don't have their origins at least partially in Tolkien. Not that D&D Elves, Dwarves, Halflings, and Orcs are the same as Tolkien's, but the influence is there, and LotR is as much as ever a lot of people's first experience in "grown-up" fantasy (as opposed to fairy tales, etc.)
2) as someone mentioned, there isn't a real strong archetype for gnomes. Third edition helps a lot in making them distinctive, rather than being junior-grade dwarves who also can do a little illusion magic. Dragonlance took Gnomes in a direction that has had some effect on how people view gnomes (although precious little on the official write-ups).
3) They don't really seem to fit in with the traditional adventuring party. All the material in the PHB and such continually describes them as homebodies. Homebodies do not great adventurers make (Bilbo Baggins to the contrary). In a party set up as defenders of a location, rather than explorers of the unknown, they'd probably work better. They seem somewhat out-of-place in urban settings too, which limits their proper place even more. Maybe in a "defend the small town and enchanted forest" campaign there would be much for a gnome to do.
That being said, I like gnomes. my first 3E character was a gnome. I feel we need more situations where they will fit.