The problem is that it's two arguments at cross-purposes: Faith versus evidence-based practice.
Rewinding to what Heartbreaker mentioned that JP says that atheists aren't happy, despite the fact that it's yet another assertion that JP likely pulled out of his ass, let's argue the point as if it's true. I would argue that theists are at least as unhappy hence they decided that God is real along with the belief that he's a kind, all-wise, all-knowing God who has their back. It comes down to that notion that some people would prefer to embrace a comfortable lie rather than the uncomfortable truth: In this case, there is no God. Therefore, theists are not altogether happy because they know at heart that their comfort is a lie, and atheists are unhappy because the world is as fucked up as it is and there's no morality-based afterlife that dishes out what people supposedly deserve.
Douglas Adams also stated that many solutions were proposed to the unhappiness problem, but those solutions tended to revolve around small green pieces of paper (which was odd because the small green pieces of paper weren't unhappy)...