I do see your point regarding places that someone would go to explicitly for condoms - but the big bowl was in the study room for a college program. Almost all the people in the program were there everyday condoms or not - so maybe the solution is to put them in places where people already frequent?
School/work/etc.
Because I do agree that not many people are going to make a trip to Planned Parenthood, park, and go in just to get some free condoms.
I don't see a problem with condoms from a public bowl. I used them throughout my freshman year without a problem. As for your embarrassment factor, that's a problem regardless of free or paid. That's just the stigma around sexual activity in general.
Besides, I don't want to use condoms that came from a bowl at a public place. I remember the first time I bought a bunch of condoms at a young age, not only was it terribly embarrassing and expensive at that time (I wasn't working, try explaining to your parents you need money for sex), it wasn't fun hiding them from my parents either.
I imagine this is a bigger problem for women - imagine a mother finds a dozen condoms in her 15 year old's purse.