My friend, there's no difference at all.
PayPal are merely conduits, but conduits whose 'security' comprises of just a username and a password - yet there is an open door, direct into your bank account. If that 'security' (I seriously laugh) is compromised, then it's an open chequebook to defraud anyone of any single sum of money you so wish.
The problem, is about conduct and behaviour. Prior to this episode, I'd been a user of both PayPal and eBay - respectable sums of money passing through both, over a lengthy period of time. If one of your customers tells you that you're the victim of fraud, then it pays to sit up and listen to them. What you DON'T do, is ignore them, treat them like a criminal and then call them liars.
I now advise people to stay WELL CLEAR of PayPal. PayPal is marketed as being an easy way to transfer money. Yeah, it is - too easy, and too easy to be scammed on, and very hard to get your money back. The problem is though, you just don't think about it, do you? Yet, look at how much banks spend on online security; pin codes, tokens, pensentry, etc... And yet, if you're on PayPal, all of that security can be compromised with a mere email and password. Bang - direct account into your bank account.
A lot of internet sites use PayPal these days, but I'm happy to ignore using it. It isn't safe, it isn't secure and - worst of all - they treat you like brick if something goes wrong. That just aint good enough.
