Anyone who's ever taken a phonics class in elementary school knows that the sound /f/ in English is regularly spelled 'f' or 'ph,' with a few exceptions like the 'gh' in 'laugh.' And anyone who knows anything about etymology knows that the words with 'ph,' like 'phone' and 'sphere,' are of Greek origin, or from other languages that came to us through Greek ('Caliph' from Arabic and 'Seraphim' from Hebrew). But, the question is, why the hell do we transcribe the one letter phi in of Greek as 'ph' and not 'f'?
The answer is that originally, this sound was not the same as /f/, the labio-dental fricative, but it was in fact the aspirated voiceless stop /ph/, like the 'p' in English at the beginning of a word. This sound is quite different from the 'p' of Standard Average European languages. Ancient Greek had contrastive aspiration, which is not found in modern European languages, including Modern Greek.Depending on what period or dialect of Ancient Greek was being spoken, it could also be the voiceless bilabial fricative /φ/, which is pronounced by putting your lips in the same position as /p/, but forcing air through and not stopping like you would for /p/. It should sound something like simply blowing air through the lips. In either case, it was not the /f/ of Latin the languages which adopted the Latin Alphabet.
Of course, in modern Greek the sound is now /f/. This is because the sounds have evolved for reasons of ease, contact, or other historical reasons. Study of how these changes happen is one of the fields of historical linguistics. Interestingly, the same thing happened with other fricatives in Greek, and is reflected in the spelling of English and some other languages which use the Latin Alphabet.
Theta, the voiceless interdental fricative /θ/, was originally /th/ (of course, in English, fricating /th/ would give us /s/ since it is very alveolar, but in most Standard Average European languages, /t/ is a dental sound, which would yield the interdental /θ/) , and chi - the voicless velar fricative /x/ - was originally /kh/. This one is spelled 'ch,' like in 'chrome,' and this is because the Latin letter for /k/ was 'c.' In fact, the letter 'k' only came into the Latin alphabet to distinguish /k/ from /kh/ and/or /x/.