I just used miles with Alamo for a week-long rental at MCO, the total due at the counter was $0.

You'll probably have to call the specific rental company local office to find out if there are levies that are not covered by the miles at that location since that would seem to be the most likely kind of "taxes and fees" that wouldn't be covered (and disclaimed) - example local mandatory tourism service charges or usage fees for the rental car a.k.a. "recovery" fees.