The biggest enemy to your PVC raft is UV radiation from the sun. Make sure that the cover you use is opaque to UV. For example, a piece of clear plastic sheeting will leave your raft exposed. And don't assume a $10 tarp from the local big box store will do the job either.
Moisture could also be a problem. That might sound funny, given that it's a raft your asking about, but what I mean is that water expands when it freezes and can cause damage. In the world of geology, this phenomenon is called frost wedging and is a significant weathering process. In other words, the freeze thaw cycle could be hard on the welds and valves by exerting hydraulic pressure on them in a way the designers of the boat didn't intend.