Not all of the Uchiha were in on the revolt. From what we've seen, it was actually only a small part. So for Danzo to execute the whole clan for the workings of a few would be like killing all Somalian's because a few are Pirates.

Also, a quality of being a good leader is having people trust you and your judgment. Who trusts Danzo? Hell, even his brainwashed lackey Sai is having doubts.