There were a couple of reasons:
1) the Africans looked a lot more different from Europeans than the native Americans (so they could not "blend in" so easily
2) The natives would have an incentive and a place to run away- and a support of a whole tribe. But once you shipped the Africans away from their country, there had no place familiar to them to hide in.
3) Europeans and Africans already shared immunological defense to the same diseases