I keep it in my (front) pocket. I do, however, not mix it with keys or coins or something like that.
And yep, cases can cause damage too. An easy example: you put your iPhone in a case, somewhere along the road some sand manages to slip between some seams, and guess what happens: there is some friction and the sand scratches the phone.
I wouldn't be too worried about some scratches though. It's an object you'll use for the next two to three years and at some point, you're bound to scratch it.
Also, keep in mind that the iPhone 5's back is mainly made out of metal. Aluminum can scratch. But as I said earlier: aluminum might scratch easier than glass, but glass breaks much, much faster than aluminum.
That said, I'd rather see an iPhone 5 drop than an iPhone 4S knowing that the entire back of an iPhone 4S is made out of glass.