Been on eBay since the beginning as a buyer and seller, 1000+ transactions with 100% positive feedback. Never had a single problem in all that time. I posted a comprehensive eBay buying guide for trains a while back, but after putting many hours into it, the thread was deleted. More than anything, just be aware that there are many types of sellers out there--know which you're buying from so you know what to expect. At one end of the spectrum, you have those who are selling to put food on their table, and at the other end are those who don't NEED to sell anything at all, so they'll put a Buy-it-Now of double MSRP just to see if someone will bite. There are many other selling styles along that spectrum. YOU are in control of who you purchase from, just like anything else in life. If you see blurry pictures, vague descriptions, or something feels shady, just don't go there.
The best prices to be had for trains on eBay are from private sellers who are unloading a collection. They don't care what they get for the item, they're just trying to get rid of it. Search ALL eBay for the item you want (not limited to the trains category, as people often mis-categorize listings), choose to view AUCTIONS ONLY (exclude Buy-it-Now) and sort results by price, low to high. Work your way down the list of results, and add things to your watch list as you see fit. Note the auction's end time and place your bid in the closing minutes. You won't win them all.
eBay takes practice--in the early days, I often overpaid because I thought it would be my only chance to get something rare, which was never the case. Now when I sell, it's only because I don't want the item anymore, so everything starts at 0.99 and sells for whatever it sells. Those are the folks I buy from as well.
eBay is almost never a good vehicle for purchasing newly-released products. Think about it--what seller is going to buy newly-released products from Lionel/wholesaler and sell it for a bargain when they've got eBay fees also taking a chunk out of their margins? Develop a relationship with your LHS or a forum sponsor for new stuff.