The (relatively easy) approach I've taken is securing the services, and granting permissions to a role/user on the local domain. I then secure the folder my Flex app will go into using IIS (using Active Directory). Finally, I generate a token using that user for the secure services, and use that token in the Flex app (both for operational layers and any widgets like Search) that goes into the secure folder.
The downsides: 1) you have to remember to update your tokens at least once per year 2) it's not especially user friendly to require a login before the page even loads (as you have no opportunity to provide instructions on what login to use).
The upside: it's pretty fast, easy, and simple.