Nice well thought out post QC. A few points:
Your example is different (to me) because of the bailout. That money should have come with stipulations and restrictions. Maybe the gov't couldn't get around those bonuses if the employees had a contract with it in there or maybe they didn't even address it. I agree though that it's galling to see OUR money being used in that manner.
It also begs the question on whether the Feds should be involved at all in bailing out any business (looking at you GM)...but that's another discussion.
If someone starts a business then they take a risk while using their money (or money they're responsible for). They provide jobs that we all desperately need...but they aren't required to be pillars of the community nor to have the community's best interests at heart. By (over)taxing them you might get some of the money they'd not so smartly spend (it is their money), but as you agreed if they can pass it on to the consumer you can bet your bottom dollar they'll do so.
In a nutshell...it's their money. If you want to make sure and tax those guys close the loopholes/tax breaks and set a flat tax. I'd warrant that the gov't would get at least as much that way as the status quo.
What they REALLY need to do is stop spending millions watching worms have sex (example). The Feds have no business spending MY money on bullshit like that.