Don't know about anyone else, but to me, using Geronimo's name for this mission did nothing but point out his role as a respected warrior in this country.
It surely did not imply he was any kind of terrorist, but rather, that he was the kind of warrior we would choose to defend our country against terrorists.
Same goes for naming sports teams with Native American references. No one picks a name they feel is derogatory for their team. On the contrary, they pick a name they think embodies the fierceness and victorious aspects of their team.
Some times the caricatures of the mascots are not in good taste and, no doubt, the team franchise and name are commercialized, but the choice of the name is never guided by derogatory intent.