*sigh* why do people think yes man is evil or has a hidden agenda? He was created by a Follower!
Straight from the wiki...
â– After the assault on Hoover Dam, Yes Man informs you that he found pieces of code within Mr. House's mainframe that "changes [his] personality" and says he will seem to be offline for a little while until his personality change is complete (he never actually shows his changed personality due to the game ending). Part of the change is that he's going to be more "assertive", hinting that he will no longer be under the Courier's control. It appears that this may have been a fail-safe implemented by House to ensure that the city he loved would be in safe hands in the event of his death (basically making Yes Man able to fill Mr. House's role as he has all of his data on the network).
So it's either House screws you over or Yes Man becomes Skynet.