I use my Giant TCR Alliance on the trainer and it's been fine thus far; it has a carbon fork, top tube, and seat stays. Btw, as of '11 Giant no longer makes an alu/carbon mixed bike (well, they still do carbon forks on most if not all their alu road bikes).

If I had anything nicer I probably wouldn't use it on the trainer regardless of what it was made out of but that's just me. I've heard that some manufactures post a warning about using certain bikes with trainers and that it may void the warranty but don't quote me on it.