OS X 10.11 El Capitan removes the legacy Java 6 SE runtime, which is required for Flash Builder 4.7 to run. Are there any plans to update Flash Builder to prevent this problem? At the moment there is a workaround which bypasses the OS X Java version checks in order to reinstall Java 6:
Resolved - Apple Java 6 for 10.11 | Page 2 | MacRumors Forums
But this isn't a very good solution...