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1) While I'm not 100% sure about the answer to this, I think there is a way to decompile a SWF. I assume it is your base code that you want to protect, or is it the application logic? The thing to be clear about is that Flex is the presentation layer in your app, your back end logic will be served from web services, java or ColdFusion. I use the latter, and thus my business logic is protected. Does that answer your question? Can you clarify your concerns?
2) Flex is browser (on-line) based. If you want to port it "off-line" you will need to look into Apollo. I'm not in a position to tell you what you "lose", if anything.
3) I'm not sure exactly what you mean - are you talking about authentication? It handles as well as any other language.
4) You'll have to explain your requirements better - It sounds like you need some sort of role management within your app. That is something you'll have to code. The good thing about Flex is that you can't URL hack to different pages, like you would on a HTML based site.
5) I would use CSS. As of version 2.1 of Flex, CSS at runtime is supported.
6) Flex apps are rendered in a browser, and are cross platform to MAC's.
SoThink has a SWF decompiler. It will only work with versions 6-8 at this time though so it wouldn't work with Flex-compiled SWFs which are version 9 - even if it did would only give you an FLA file and not MXML. I have not personally tried it but I have been told by friends that it works. They have some other nice tools I have tried such as their DHTML menu which will create dynamic menus from data queries and works well with Coldfusion for example.
Find it at http://www.sothink.com/product/flashdecompiler/index.htm