It definitely can help you pursue any victory condition but you have to choose your beliefs and how you spend your faith wisely. I also tend to neglect it because it's so hard to found a religion on Emperor and up. My current game with Spain is so much fun because I'm trying to spam Catholicism everywhere while steamrolling Conquistador-evangilization-brutality everywhere, converting as I conquer. Pretty awesome. But I agree it's not the most obvious or appealing system in the game. Still, given a fair share of attention it really whips the llama's ass.