It's called political compromise. Bush wants to ban it, but at the same time he knows there is no chance in hell an outright ban of all future stem cell research would get past congress. So, he does the next best thing and take away the fundings.
I'll lay down hard money that Bush doesn't give a crap about it one way or the other, but knows that making it a political issue will generate votes.
"I know some of you are going to say 'I did look it up, and that's not true.' That's 'cause you looked it up in a book. Next time, look it up in your gut."
-Stephen Colbert