It's not rude to tip. I'm sure every server is happier with a $6.59 tip than no tip. They may find it annoying to get change when they cash out, however.

I personally always just round up in these circumstances. The difference between at good tip and a great tip is not much, and who cares about the extra 41 cents? If your employer is going to make a stink about 41 cents perhaps it's time for a new employer...or a review of policy.