In "Deadlock" Boomer and Ellen Tigh arrive at the Galactica. Tyrol identifies Boomer and Adama has her thrown in the brig. Later on in "Someone to Watch Over Me" the rebel Cylons request Boomer be extradited to answer for her crimes (siding with Cavil and going against her line).
There seems to be quite a lot of anger against Boomer from the Colonials, however, it has already been established that she wasn't aware that she was a sleeper agent and that she was programmed to shoot Adama.
The only thing that the Colonials could be angry about could be their experience on New Caprica, but it was never shown that Boomer did anything particularly awful (or was it?). Caprica 6 seems to be more accepted by the fleet, yet she jointly led the Cylons to try to live together with humans.
Is the anger explained anywhere ? A Webisode perhaps ?