Ultimately, the biggest reason gnomes get left out is probably Tolkien. The Lord of the Rings is certainly not the only influence behind D&D, but it is one of the strongest, especially where races are concerned. The stereotypical D&D human, dwarf, elf, and halfling are essentially watered-down derivatives of Tolkien's humans, dwarves, elves, and hobbits.
Furthermore, gnomes WERE belatedly tacked on to D&D (as far as players are concerned, at least). If you look at Basic D&D, you could play a (human) fighter, cleric, thief, or wizard, or you could play a dwarf, elf, or halfling. No mention of the gnome as a PC (and the monster entry basically portrays the gnome as a short human-like dwarf).
For those of you looking to strengthen the presence of gnomes in your world--you might wish to look through the "History of Middle-Earth" series edited by Christopher Tolkien from his father's notes. Tolkien's original notes does have a race of gnomes mentioned....been a while since I've read them, but I believe the gnomes eventually became either the Noldor or into the "dark" elves (e.g. Eol). Either of these possibilities would add a lot of distinct flavor to a D&D gnomish race.