I've always run my Android phones naked. Droid 2, then S3, now S5. I'd gotten a couple of scratches on my S3 from 2-3 careless drops onto a wood floor, mainly pulling my phone out of the case when in a distance room in the house and running to frantically get to it, pulling it out of the belt case, and answer a call (I take it off my belt when I get home fyi). The scratches though were completely unnoticeable when the screen was on, could only see them at certain angles when the screen was off, so it never affected performance. But I never get scratches any other way since I keep it in a belt pouch, and now I don't frantically pull out the phone in a rush to answer anymore and have been more careful anyhow. My Droid 2 I never got any scratches on.
For me, nothing matches the smoothness of sliding across the glass, even glass screen protectors still feel more "sticky". So naked and careful has always been my choice and it's worked for me for 4 or so years now.
Rev.