Peter Lacy is pitting Apollo/Flex vs. the web. Please don't. That is mistaken.
Adobe "gets" the web. These components run "on" the web, and are "of" the web. Yes, they have ways to use things in a non-web way, just as Java and C# have. But they fully support the web, just like Java and C# do. They are on, of, and for "the web".
Here's how you do it: write the server as if any kind of web-able client could consume it. Write the client in Apollo or just Flex to consume that server's resources.
OK? That is not "versus" the web in any way, shape, or form.