Kennedy was Catholic. That made some people uncomfortable, because we had never had a Catholic president before. Some people—a small minority of bigoted Protestants, in my estimation—argued that a Catholic president would have a stronger allegiance to the pope than to the constitution, etc. But I think that issue was pretty well put to rest during Kennedy's campaign. I can't remember it ever being an issue once the election was over.

Oswald was an avowed Marxist, so I assume he believed as Marx did, that religion is the opiate of the masses. I don't know whether he was brought up in any religion. I think Marxism was something he discovered on his own; his mother didn't teach him to be a Marxist. (His father died before he was born.) I don't think an atheist would care to make much distinction between Catholic and Protestant.

Jack Ruby's original name was Jacob Rubenstein. I assume that means he was Jewish by heritage. I don't know if he was religious. His parents were immigrants from Poland.

I don't think religion had anything to do with the assassination, although Oswald's motives were never made clear. It's pretty clear that Ruby acted on impulse, and he was motivated by outrage and sympathy for the Kennedy family. He seemed surprised that he wasn't treated as a hero for killing Oswald. Conspiracy theorists might argue about this, as they argue about everything to do with the assassination.