I think eBay should just ban the use of the word "rare" in auctions. It doesn't mean anything there now.
As for the bubble... I wouldn't place the blame for that on eBay so much. It wouldn't matter if people were selling on eBay, to a comic shop, or at a flea market. The real reason behind the pop was overproduction when the bubble was growing.
People looked at comics and collectibles as an investment because of news stories of old comics like Batman #1 selling for $25,000 or similar prices. That's why people started buying comics as an investment - they thought that in a few years, their shiny #1's would be worth $25,000, too. They didn't stop to think comics used to be printed in smaller quantities or that it took Batman #1 60 years to reach that price.
The comic companies took advantage of the investment buyers to make a lot of money by producing tons of books to meet the demand. Books like X-Men #1 in the 90's were printed with five covers or flashy holograms or foil. Gimmicks designed to increase demand that worked at the time.
The bubble popped because when people tried to sell off the things they had bought for a return on the investment, they did so way too early. Everyone else had already bought the same things and still had them. Then people decided the investment was worthless and stopped buying. By then, the comic companies were still producing in higher volume, so they were left with a lot of unsold product and hit some hard times.
In fifty years, those X-Men #1's may be worth something because a lot of them will have been destroyed by people thinking they're worthless. But it'll take a long time for that value to rise.