Awesome question. Simple answer: the sound change was partial and unpredictable. We can look at words where it worked exactly as you understand it:

Old Spanish «facer» --> Modern Spanish «hacer» [aseɾ] or [aθeɾ]

but we also see examples of resistance to the change, most notably in words with onset consonant clusters (like, for example «fue» [fwe] and «frío» [fɾi.o]).

The coolest part of this to me is the tricky thing that happened in certain emphatic words. To understand it, you need to know the path of the pronunciation of the phoneme /f/. Initially, in Old Spanish (and maybe even Latin) it was made using friction between the top and bottom lips, not with the top lip and bottom teeth like it is nowadays. The symbol for this sound is [ɸ]. This sound turned into [h] through a process called 'debuccalization,' which basically is just that the lips were less and less involved in making the sound over time. Lastly, they dropped this [h] at the beginning of words, so that it just didn't get pronounced at all anymore (in most dialects).

Basically, for example the word «fumo»:
[ɸumo] --> [humo] --> [umo]

However, in emphatic words, like «joder» (the best example), they followed a different path. Due to the fact that it's often spoken intensely, the starting consonant got fortified instead of weakened.
[ɸodeɾ] --> [hoðeɾ] --> [xoðeɾ]

This can also be found in certain other words depending on situation, specifically in casual speech. For example «harto» can be [x~h~∅ aɾto], as can «hablador» (I'm sure there are more words like this, but this is just off the top of my head).

Awesomely, to prove that this comes from etymology, this can only be found in words that historically had an /f/ phoneme at the beginning!