Under the terms of their marriage contract, Mary was acknowledged as Queen Regnant and Philip as King Consort. The English peers did not want a Spanish king ruling England, although there was little enough they could do about Mary and Philip's potential progeny.

The contract set up that Philip was King "by right of his wife," and that all Parliamentary declarations would be made using both of their names; and that his sovereignty in England would only extend over the course of her lifetime.

The nomenclature was adjusted when Albert and Victoria got married--he was given the title of Prince Consort, rather than King, to eliminate the kind of confusion that you're experiencing right now. :-) But at the time of Mary's reign, there was only one Prince in England (the successor to the throne), as all of the other male children of a monarch were styled dukes; so this solution to the Regnant/Consort nomenclature problem wasn't as immediately obvious as it is to us now.