I guess my simple explanation would be that it some cases it sounds more like [fu] and sometimes it sounds more like [hu]. It also falls into the "h" line on the syllabary chart, and I think as a result the convention is to transcribe it is as "hu" so it fits the other syllables in its line.
To be more specific, I think it is pronounced more like [fu] especially in foreign words to replicate the [f] sound, since the natural way to produce this sound is to make it sound more like a cross between [f] and (and the fact that it sounds like both is also maybe a reason why you could transcribe it either way). For example, ファスト・フード. I think Japanese would tend to emphasize the [f] component of the articulation to make it sound more like the way we pronounce 'fast food' in English.
However, I am not an expert on Japanese phonetics by any means, so maybe someone else knows better than I do. I am merely speaking from my few years of experience in Japanese language study and linguistics study.