I've used eBay for years and I'd estimate that I've gotten at least 400 figures total using the website. Out of all those figures, I think I've had a total of 3 or 4 bad experiences.
So yea, the vast majority of sellers on eBay are actually honest, good people. However, there will ALWAYS be a couple of douches who screw you over. But that's in pretty much every walk of life.
The bad experiences I can remember is having a guy sell me a TM2 Megatron claiming that it was complete, yet it was missing all of its neck scales. Another guy sold me a "mint" Powermaster Prime that was yellowed and had rusted screws. Had one guy take 3 weeks to ship an item out to me, and someone else sold me an Energon Ravage only to have Energon Perceptor come in the mail.
But there have been really good experiences as well. I had some dude sell me a TM2 Jawbreaker that was supposedly mint. When I opened the package, it looked like it had been through hell. Paint chips, flaking chrome. You name it. I told the seller about it and he immediately refunded my money. That's just one of a few bad deals that were worked out easily.
Like I said, though, the majority of transactions are smooth as silk. But I'll knock on wood since I have 2 very expensive packages coming in the mail this week!