IANAE (electrician), but per my understanding, putting copper cable inside a PVC (or other plastic) conduit is among the worst things you can do; it gives the strike only one place to go: down the copper.
EDIT: I found a comment on a CCTV forum site that corroborates this: http://www.cctvforum.com/viewtopic.php?p=79496&sid=0e2686464...
This also goes for ethernet between buildings. Surprisingly enough if the building is poorly grounded the best path can be over your ethernet to a different building.
The ethernet transformers don't really help. They are just another part to get melted off the circuit board if there's a close lightning strike.
Surge protectors pretty much exist as a sacrifice to protect your more expensive electronics (switches and routers).
http://ask.metafilter.com/57840/What-kind-of-network-cable-t...
Ground loops shouldn't be a problem as the APs have transformers that don't use ground at all so there's no ground connection to mess things up.
If lightning is a big issue you might need surge protectors on the lines. Is a Cat6 cable inside a plastic conduit that susceptible to getting hit by lightning though?