They took "Bonneville" off the car (as well as the names of some other GM vehicles also) for marketing purposes. The reason being, the name "Bonneville" conjured up images of clunky, lumbering, snoozemobile barges of the 70'* and then into the 80'*. As such, scaring away potential "youthful" customers.
Heck, my GTO doesn't say "Pontiac" on it anywhere. For '05/'06 that changed, but they wanted to get potential BMW/import people to look at it and they thought that having the Pontiac nameplate on it, would scare them away or something due to the "image" GM products have had over the years of "lesser" quality. At least that'* what they claim anyway.