You can use the Packager for iPhone to get Flash content on an iOS device. However, you can't download compiled Flash files (.swf) to the iOS device and execute them after the app has been installed.
From the developer documentation:
Loader
In an iPhone application, you cannot
use the Loader.load() method. However,
you cannot run any ActionScript code
in SWF content loaded with the
Loader.load() method. However, you can
use assets in the SWF file (such as
movie clips, images, fonts, and sounds
in the library). You can also use the
Loader.load() method to load image
files
If you would like to use InDesign and some of the other tools that Adobe Makes, you can consider the so called Digital Publishing Suite which is a toolset that was used to make some of the iPad magazines such as Wired or Martha Stewart Living.