Most of the horrible stories we hear about Columbus (and that have circulated once again this October 12th) come from one primary source, the investigation of Bobadilla. Interestingly, most of the deeds described in these papers were against Spaniard subjects rather than Indians.
Considering that Bobadilla was the one that gained the most from Columbus' demise (since he was named Governor of the Indies), can we trust his reports?
There are numerous reports about Columbus' cruelty, even excluding Bobadilla. The Dominicans were investigating him around the same time and his own journals talk of some of the brutality. Bobadilla focused on Spanish subjects because those were the people that mattered to him, he wasn't a saint either. There are several sources discussing this in a previous thread