Humanity has had religion since we were still reproductively compatible with chimpanzees! A little thing like travelling the stars won’t change that. It might change the religions — but so do a lot of rather more terrestrial details.
The thing is, there will always be things that science can’t really explain. Sometimes you just have to believe it’s the Spirits, the Gods, the færies … and, the thing is, maybe it’s true. Plenty of physics do go into other universes — whether by design or mistake, who’s to say our universe wasn’t built by another intelligence from beyond the borders of this reality. Would they not be the Gods, the fæ?
It is no more realistic to believe that humanity will be monolithically atheist than to believe it will be monolitically Methodist. True, you could put an explanation in, and maybe they will be universally something; why not, it worked for medieval Europe.