I've recently had a couple of customers choose not to use the .Net 2.0 Membership system for user authentication in favor of a home-grown solution. The decision was based on time-to-market using an older solution they had each developed independently. At the time I wasn't comfortable prolonging the life of legacy infrastructure. And, now we can really see that adopting the new model as soon as possible is a good idea.
Scott Guthrie points out that SharePoint 2007 and Commerce Server 2007 are built directly on ASP.Net 2.0 API's. So making portable web parts is easy and highly leveraged across potential solution spaces. Moreover, using the new Membership Provider Model for authentication gives you flexibility to easily adapt your applications to a future or shifting enterprise archiecture.
For example, build an ASP.Net application today, port it into SharePoint 2007 tomorrow, then build a custom Membership provider for better authentication and identity management within the enterprises and see the benefits across all of your applications.