Most Greek/Roman gods and mythological characters are more widely known by their original Greek names. Why isn't that the case with Herakles?
I don't think there is any detailed source on as of why. From what I have seen though, the reason it is more familar with the general population is because there is more Roman literary sources that mention Hercules than there is Greek literary sources that mention Herakles. You'll find even within translations of books such as the Odyssey by Homer that it is spelt Hercules as well.
It's really just a matter of preference as of which one you use. Hercules is the Latin version whilst Herakles is the Greek version of spelling.