Ok, it was subtle reference, and didn't detract from the movie, but why is there any reference to God in a Star Trek movie?
If you're a Trekkie, and haven't seen the new movie yet, you'd better go soon, or you'll be the last person on the planet, and maybe off-planet too, who hasn't seen it yet.
Even with with modern filmmaking techniques and great special effects, it is amazingly true to the original concept. I thought the new actors for the most part did a fabulous job recreating the original roles. Zachary Quinto (Spock), Karl Urban ("Bones" McCoy), and Anton Yelchin (Chekov) were remarkably true to the original characters, yet brought fresh blood to the concept. But Chris Pine (Kirk) was the star, he was true to Shatner's original character, but without the over-the-top Shatnerisms that we know and love.
And the screenwriting was great, special effects and editing, all marvelous. I was a happy Trekkie!
But they had to throw in that one little line, "Godspeed." I can't even imagine why. Why not "Good Luck," or "Take care of yourself"? I suppose it's because the writers, actors, and director, unlike the advanced, highly-scientific civilization they portray, are not themselves scientists. Good writing and good directing are not related to good science or a rational view of the universe.
It was no big deal, but it was completely out of place in a movie about a future that has moved past illogic and superstition.