I park outside with a cover also. Had the same thing happen, melting on exhaust tips, after using the cover a few times. Solved the melting problem by hooking the back edge of the cover over the top of the bumperettes when the exhaust is hot and then pulling it down over the back of the car later on, after it has cooled down (if I remember to do it

).
I was just looking at Covercraft's web site and see that they offer a Nomex and Kevlar option to protect the exhaust area of the cover from melting. The catch, $150 extra cost added to the cover.
Then I got inspired by the "Nomex/Kevlar" materials. How about slipping an "Ove Glove" over the exhaust tip. Might need 2 if you have a 'S'. It'll protect the cover from the hot metal.
http://www.ovenglove.net/
$16.00 at Walgreens and Amazon.com has a version called the Handy Man's Ove' Glove for $14.99
After thinking about the glove possibility, I would turn it inside out, so the Nomex/Kevlar side is next to the hot metal, not the cotton inner liner. Cheap solution to protect the $$$ cover.
If you forget to take it off, I'm not sure how long it would stay on the exhaust tip, but it sure will look hilarious going down the street.