Echoing the comments above, the trainer's braking force greatly affects how the trainer feels. If the wheel is moving slower, then the trainer has a higher braking force. A higher braking force means that you are experiencing more force throughout the pedal cycle, which causes more muscle engagement at top end bottom end of the pedal stroke. This will wear you out faster than lighter braking force against a faster turning wheel.

Edit: GPLama illustrates this in one of his videos by showing the power phase differences in the pedal stroke as a function of gearing on an ERG smart trainer.