If you are using the web-tier compiler, also known as the Flex module for Apache and IIS, you can request an MXML file that has not yet been compiled into a SWF and have it return only the SWF file (without the wrapper). You do this by appending *.swf to the end of the request string that specifies *.mxml.
For example, the following request returns only a SWF file and no wrapper:
http://www.mysite.com/flex/MyApp.mxml.swf
For more information, see Using the Flex Module for Apache and IIS.