I owned a server running 2003 and iis6. I never had an issue. Your users are stored in an SQL DB of which you as a vb.net developer should know how to right asp code that will allow a call back from a transaction from ccbill. There are plenty of sites out there using them. The only time I saw a need to make local user accounts on the box itself was when you are using a PPM (Pay per minute) system with windows streaming media server. You need a local account in order to really track the access and for how long. That's where your own plug in comes in.
As far as security I have never seen a problem. I used software called whoson.com. It tracks known website hacks and will automatically ban the ip or the range from IIS after a certain amount of attempts to "get or push" the file/files. IIS6 in it self is very secure. I'm sure websites from both platforms have been taken down or defaced. I would think more Linux boxes though being windows servers for websites and hosting companies are not the norm. Mostly due to price and myth of a bad OS. Don't let vb.net hold you back from doing work on pay sites and surly don't let a crappy reputation limit you.
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