If the floor is not perfectly flat, the toilet will rock and the wax seal will be compromised. In this case the toilet must be shimmed to prevent it from rocking, but the shims can be installed in a manner that will allow the toilet to be level.
The problem that might exist when one does this is that the gap between the floor and the toilet becomes greater, to the point that it may look bad. When I have needed to shim, I try to keep all the shims in near the back of the base so that the front of the base stays on the finished floor. If the floor is really screwed up, then more drastic measures are in order.