Can I put a zener diode *before* PTC to protect the supply?
Your thinking works, but seems unnatural. Why is the 5v likely to get connected to 12v?

Personally I would put ptc fuses on the output of any user accessible 5v terminals, as well as a standard fuse and voltage clamp on power input the normal way round. 

Incedentally, a zener diode is not the right component for this. check out tvs diodes for overvoltage psu protection