There are no "good guys" in a conflict between religious people.
Religion does play a role in the conflict, particularly over the question of where the border between an Israeli and Palestian state should go (so that holy sites end up on the appropriate side), but I don't think it's very useful to understand this as a religious conflict.
The Jews who moved to Israel in the early 20th century weren't pilgrims. They were refugees fleeing political persecution. The founder of Zionism wasn't even religious.
And Israel didn't happen because religious Jews enthusiastically got behind the idea of Zionism. Israel happened because Britain got behind the idea of Zionism.
Because the Crusdaes of the 11th to 13th centuries still loom large in Western culture (Richard the Lionheart and all that), I think Westerners have a tendency to think that the situation in Israel/Palestine is a continuation of those conflicts. But it's really not. It's a 20th century creation.