Because it was easy to assume that the sub stayed above water for much of the journey, or that Indy somehow snuck on board while no one was looking.
And because the raft escape was not only an inspired solution, but looked like something that just might be plausible (and was proven
to be so on an early episode of Mythbusters).
Neither were as ridiculous as a human being surviving both a nuclear blast
and the gigantic impact of a fridge hitting the ground multiple times.
(Although to be fair, I was still willing to go along with the movie at that point; it was only after a multitude
of similar, ridiculous scenes that the movie finally lost me)