An Ibuprofen bottle is very distinctively different than orange pill bottled. For all he knew I had cancer. Would that still have made his "joke" okay? Not in the least.
I keep mine in a plastic baggie. Always have a minor freakout at the airport where I realize that's probably not a good idea and debate tossing it out to avoid questioning. 
Okay, that makes a little more sense.
So the real etiquette is allowing people to make offensive jokes to me and for me to not respond in a way that lets them know it isn't appropriate? How is him saying "There's no way you need all of those!" in an accusatory tone any different than someone saying "You're too young to be using the handicapped spot!"? It's not, at all, he's making an interesting assumption about my health.
His first comment could have been a joke, and I suspect it was; my response came out more as a question (imagine it like this, "Well...that's an..interesting assumption?"). His second comment immediately turned into a grilling tone of voice as if I was in an interrogation room, his demeanor changed from possible joking to definitely wanting to know what right I had to have my medicine in my bag (I've tried explaining it other ways, but maybe I wasn't getting it across). How is that at all appropriate? It's not, and I still don't see how you (a number of you, so no one specifically) can think it is. He was saying rude and offensive things and I responded in a way that let him know to stop, which is the point of the phrase. At what point is it okay to act like he did towards me? It's not, it just isn't. If only the first two things had been said (his comment, then mine) I wouldn't be posting here because nothing egregious happened. It was the following exchange that turned the tables.