Can anyone tell me whether code on the timeline is harder or easier to steal/decompile? Or is it all just the same?
There's no real difference. A dedicated programmer can always get to and reverse engineer your ActionScript. Bear in mind it's not just 3rd party apps like Sothink that can be used. Even Adobe have a tool for 'inspecting' a swf: http://labs.adobe.com/technologies/swfinvestigator/.
If your code is genuinely special enough to warrant stealing, then you would want to use a platform other than Flash (or put your sensitive code into an external C/C++ assembly and run that using something like Alchemy).
Are you really doing something so unique that people are going to try to steal it, though? Is it so special they couldn't just figure out what you've done and copy it?