I'm sure it's done to cut down on counterfeiting. Many people juts don't understand how the banking system works, and these people make easy targets for scams. As has been noted in here, money orders and checks are counterfeited quite a lot, and one of the main sources of counterfeit money is transactions that take place over the internet, such as eBay.
I used to work at a bank...the problem with counterfeit checks is it's really expensive for everyone involved. It costs eBay, the seller, and the bank all money. The only person that wins is the scammer.
I had a friend that lost $1100 on eBay this way. He took a check in and they placed it on a short hold. He called to see if the check had cleared, and the bank had cleared the funds for withdrawal, so he went ahead and send off the merchandise. He did not understand that having a check clear for withdrawl is not the same as having it clear the bank totally...and the check was returned.
You could say that's partially his fault, for not understanding how the system works, and I would say you're partially true, but again, the high level of counterfeiting is costing eBay a lot of man hours, and it's costing sellers a lot of money and banks too.
Like it or not, when you send money through PayPal you've jumped through several hoops to verify your identity, and the validity of your bank account.
You can also cry murder about them forcing you to use PayPal, but again, that's done to beef up security. Since PayPal is owned by eBay, the 2 companies can work together to investigate fraud better than any other 2 companies.
There are good sides and bad sides to any decision a large company like this makes. You can cry foul, but I hope you'll take a second first to consider, outside of conspiracy theories, the reasons eBay might do a thing like this.