Tom Cruise is about 5' 6" or 5' 7" judging by the pictures you see of him in real life with other people of known height. A little bit short for an American man, but not even close to 'midget'.
Yes, I suppose it would be much easier to choose a strong actress and use technology to make her look tall rather than go searching all over for a tall actress who happens to be talented enough. But you never know if you might find a talented unknown who fits the part. Linda Carter with her classic 1940s 'Vargas girl' looks was utterly perfect for Wonder Woman. She could have been lifted from the comic.