Both film and tempered glass screen protectors will work fine with s-pen, though back when I was testing some cheap PET film screen protectors early on with my Note 2 - I found some ended up with scratch marks when using s-pen.
The main difference: film protector will protect from scratches, while glass protector will provide impact protection. The whole idea of tempered glass is to absorb the impact and to shatter (if it's too strong) without cracking your $200-$300 display. Also, the quality tempered glass protectors have a thin layer of film which keeps the broken piece of glass together so they don't spread around.