Because it fits with the English language better. You'll notice that Amun is just as often written Amen, while the transliteration really reads 'Imn'. Aton (see Akhenaton), is often written 'Aten'. Unlike with Roman Latin, which we have scribble of from Pompeii, we don't have any clue of how Ancient Egyptian was actually spoken. For instance, the vowel 'e' does not exist in Ancient Egyptian, making transliterations like 'Amen' or 'Per' (pr, the word for 'house') just educated guesses.

Edit: Figured I may as well add: There are 2 letters for our 'a', being the aleph, which roughly resembles a '3', and the ayin, with looks like ^c .