Is it the tire squeaking against the metal roller or the trainer itself squeaking (I.e. the flywheel)? You didn't mention if it's a magnetic, fluid or (probably not...) wind trainer. Depending on the trainer, you may need to just do some maintenance on it. My old Cycle Ops fluid needed some replacement parts at one time. I just got back to using it last week and had similar squeakiness that was just a result of adjustments. No matter... Better to ride the trainer than not at all.