Pretty much all of Penn between 5th and Braddock is less than optimal for riding. I do ride that section in both directions regularly at rush hour though, and rarely have problems.
The biggest problem spot I have is westbound just past the factory where the city inexplicably allows people to park on the street for a block. It's uphill and there is a LOT of fast traffic being funneled into one lane at a light. Really dumb traffic pattern. It's pretty short though and a willingness to take the lane and a bit of patience and timing will usually get you through it without a hitch.
The biggest thing on Penn is just to ride predictably and take a whole lane when you feel you need to. Some days people are courteous and you can ride further right. Some days you need to ride smack in the middle of your lane and let the bastards wait.
I've never had anyone honk at me on Penn and only rarely have I had any dangerous passes. (some unnerving ones, but rarely dangerous)
On days that I just get a bad vibe from the traffic or I am in less of a hurry I will often take Meade and/or Thomas. They are in every way better riding streets, just slightly less direct.
As for the confronting drivers issue, it's not something I've ever done. If I'm feeling zen I don't have the urge, and if I'm pissed off it's probably a bad idea for all involved. I'd be interested to see what experiences others have had though.