Just don't crank the skewer clamp down on it super tight. Just tighten it enough to hold it still while you're on it. I've seen an Al bike crack at the dropout potentially from too much tight clamping on a computrainer one winter. But then, I've seen other Al frames fail there just because. I use my carbon bike on the trainer, and it's fine. I just don't overly tighten the clamp.