It makes more sense if you realize that the sounds of the words came first (mutations of existing words from other languages) and only after the words were established in common use did they decide on spelling. And they surely did them one-at-a-time, not deciding that 'all words that rhyme or alliterate would be spelled similarly'.Why these exceptions? How did they arise?
The catch-all answer is that English came from many sources. Often the pronunciation was mangled. Sometimes the spelling was mangled to match, sometimes not.Why these exceptions? How did they arise?