The biggest problem I see, if you want to cover it, is that you either need a good cover with really good heat shield or you're going to have to wait for it to cool before you put the cover on. Slide a nylon cover against hot pipes and it will be worse than leaving it uncovered, I'd guess.
I keep a cover in my locker at work.
I bought it like most do, on Ebay with a heat resistant bottom.
It helps keep it allot cleaner in windy wet times.
i cover mine during the summer but only because i live in arizona. and buck if you have to wait for your bike to cool down before putting your cover on than you have the wrong cover. i have never waited to put my cover on and the cover touches my pipes all the time