I can't imagine saddle soap hurting the top. However, I can't imagine it providing any protection for the top either. I have a vinyl convertible top on my car and I HIGHLY recommend the Ragg Top (for vinyl) kit.
Ragg Top makes two kits one for vinyl and one for fabric tops. So, if you buy Ragg Top make sure you order the correct kit. A somewhat distant second to Ragg Top IMO is a combo of 303 Vinyl Cleaner and 303 Protectant. However, the 303 protectant doesn't seem to last as long as the Ragg Top does.