I'd take a long straightedge and see if the floor isn't flat. But, that's actually not uncommon. The important thing is: does the toilet rock, or is it steady? If it is steady, then I'd just put some caulk around the toilet. Some people prefer polyseamseal. If it rocks, call the tile installer back. He should have shimmed it so it was stable, and by rocking, the wax seal is almost certainly shot.