If you start with Flash, just the IDE and then learn how to code, navigating through frames makes sense as it's dead easy to understand/implement.
The only advantage I can think of is that objects are always there, so when you're going from one frame to another, once the objects are instantiated, they'll be there for you, so no need to remove everything, add everything again.
I'm guessing pros like Keith Peters code there views and menus 100%. Once you make your nice little game engine ( with menus and screens) ready to be reused (Asobu), the timeline seems a bit pointless for switching views. The PushButtonEngine looks great from this perspective.
If you're working with a designer, and he/she is designing the screens and the timeline navigation makes more sense for him/her while prototyping, I'm guessing there is a middle ground. As long as each screen is a MovieClip on it's own, inside the main timeline, you can set a Class for each screen MovieClip and carry on from there. If you need something to declare stage instances for you, I wrote a tiny extension that could give hand with that. Then you can carry on with the logic in your preffered IDE.
My guess is for quick additive button bashing short indy games the timeline will do just fine. If you're planning to reuse a basic engine and make more complex games, on the long run, actionscript will prove the right decision. Basic rule of thumb: Don't over complicate things without reason.