I started having foot pain a couple years ago whenever I rode. I could barely last 10 minutes before my feet were killing me. Then the pain kept on coming even when I wasn't on the lake. Long story short I had developed plantar fasciitis. It got so bad that it hurt to just walk. Trying to determine whether it was caused from wakeboarding or just from the way I walk was like trying to determine if the chicken or the egg came first.
I ended up getting relief from wearing Lynco orthotics in my shoes. They run about $75 a pair from the doctor or about $27 off of e-bay. I have a set in every pair of shoes that I wear. After about 4 months of wearing them the pain went away. My feet still get a little sore during riding, but nothing like it was before I started wearing the orthotics.
Plantar fasciitus is a pretty common athletic injury, so I wouldn't be surprised if it was caused by wakeboarding.