Well, the cosmological argument isn't an explanation based on reason. It's an equivocation based on intuition. A necessary being "causing" the universe to come into being wouldn't be like a contingent thing "causing" something else. You're treating a miracle like an ordinary cause, which equivocates on "cause." Also, "necessary being" is vacuous.
Appealing to theological and mythic poetry is handwaving in a way that appealing to theoretical physics isn't. Still, I agree that there's some funny stuff going on in the assumptions of scientistic naturalism. The atheistic notion of a law of nature, for instance, is suspicious, as I argue below.