Remember that a language is first and foremost a spoken thing, and that the word is not 女王, but [jòóꜜò], and 王女 is not the word, but [óꜜòjò]. (You could say that I’m switching one way of describing the sound with another. What I mean is that the sound of the word comes first.)
Why do we call a fireman a fireman and not a man of fire? There may be answers to these questions, but in the end, you will find that language is not always logical (especially when you get down to the morphological level), even one structured as strictly as Japanese. The words in question are imported from Chinese, and if you are interested in linguistics, you can probably find some explanation.
If you merely want to learn to use Japanese: There is a reason rote learning is used so frequently when learning words. It is effective.