The reason why the p in “pterodactyl” is silent is because the consonant cluster /pt/ isn’t allowed as the initial part of a syllable

When words are borrowed into English but have consonant clusters like this, English simplifies the cluster (in this case, /pt/ becomes /t/)

However, if the consonant cluster is preceded by a vowel, it splits up and the first consonant becomes the coda (final part) of the preceding syllable

So while it might have been he-li-co-pter in Greek, it became he-li-cop-ter in English

This also explains the silent g in “phlegm” and why it’s pronounced in “phlegmatic”