Thanks kimmibeans. I agree with what you're saying. I was super impressed by the research and resources they have there and the curators are definitely at the top of their fields. However, in the weeks since I posted this topic I have heard some things confirming my suspicion. I, and everyone I talked to, agreed that the research is great and the scientists are really intelligent, so the program as a whole doesn't have a bad rep.
However, a number of the very parsimony-centric people there, some of whom are also perceived as somewhat mean-spirited by some other phylogeneticists, are apparently sufficiently disliked so as to drag down the reputations of their students when they apply for certain jobs. I have had 3-4 unaffiliated organismal bio/phylogenetics profs at multiple schools tell me that working with the specific (very senior) people I wanted to at RGGS would hurt my CV just in terms of the social climate of the field. It's a shame because they have a super cool program, but the only people who really do the stuff I want to study are also the worst-perceived.