I just finished reading "The Mother Tongue: English and How It Got That Way," by Bill Bryson, and it's sensational--if you want to read a whole book on the history of the English language.
The answer to most questions like yours is "it just is." Most of the time you can follow that by "and nobody really knows why." That is so say, even the scholars aren't sure or have theories they can't prove.
One thing that definitely happens is that letters get transposed that would make more logical sense if they were the other way around. That is, in the case of hat/hate, can/cane, pin/pine, it would obviously have made much more sense if the second vowel were written before, instead of after, the final consonant: haet, caen, pien. Perhaps something of the same thing is true of "breathe."
Another example of letters moving is "crocodile," which is "cocodrillo" in Spanish and comes from the Latin "cocodrillus."
Another is the words that begin with "wh." Customarily nowadays we don't pronounce the "h" at all: "when" and "wen" are homophones, "where" and "ware" are homophones. However, when my mom was a kid, careful speakers did aspirate the "h" just a bit, and she was taught to do that. But--as I complained to her--the spelling is wrong. When people do pronounce the h, the sound of the h comes just before the w. They are pronounced as if spelled "hwen" and "hwere"--and they were spelled that way in Middle English! Somehow they got flipped and stayed that way--and the "h" remains even though we no longer pronounce it.
A third is the English name "Cedric." I just learned that it was originally a Saxon name, "Cerdic." Sir Walter Scott wanted to give that name to one of his characters in "Ivanhoe," but he somehow transposed the letters to "Cedric." The novel became fabulously popular and people began naming kids "Cedric" using the spelling in the book!