I usually get attacked when I point this out, but it's the way it is. I'm not suggesting that anyone should deliberately get more penalties. What I am suggesting is that if you play all out, to the whistle, and really get after it, you'll sometimes get a penalty in the process.
You should get attacked because other than strategic use of pass interference to save a touchdown against a game breaking WR aggressive penalties don't help a team out. Facemask and Targeting penalties make a team think twice about trying it in a game situation. I'd want those rules to protect my own players from injury.
You are correct that the example you give, the pass interference situation, is the only one where kids are coached to deliberately incur a penalty. What you miss is that if the players are playing aggressively, they will incur some penalties along the way, while if they are playing to avoid penalties, they will miss some plays they might have made.
I happen to like Blair Brown. I like him because he goes out out, all the time. I accept the consequence that he is going to occasionally get a penalty, but I also know that he's also going to make a lot of good plays. I take the bad with the good.
It remains true this year, as it is every year, that there is a positive correlation between penalties and wins.