A question on the roots of the word 'Pontiff'?

I quote Lewis and Short: 'pontifex, doubtless from pons-facio, but the original meaning is obscure.'

It is obviously a metaphor of some kind, though exactly where it is from is entirely unknown. I would suggest that building bridges with the gods is not an entirely Roman thing to do - the aim of religious observance was to keep the gods happy, and thus keep them away, rather than to communicate with them; it is more likely to revolve around the Tiber in origin than a metaphorical bridge. The simple answer is that no one has any real idea. Any theories there might be are entirely speculative.

Perhaps in Roman times the pontifex (as you say, ponte from pons --bridge and fex from facere-- to make) because the guy in question acted as the bridge between mere mortals and the gods.

I don't know the answer for sure, but I'm thinking that if you take it out of the literal sense, "Bridge-maker" probably meant the bridge, (or liaision, or conduit) between man and god. They were heavily into metaphor back in the day.