It wouldn't take many bedraggled homeless people to drive out the paying-near-or-above-retail customers, so my guess is that there aren't very many homeless and/or extremely visibly poor people in Clayton (or at least the neighborhood where the Panera store in the article is located).

WP says (in the demographics section of the article on Clayton, Mo) that Clayton "In the St. Louis region, Clayton is well known for housing a wealthy and educated young professional, often dual-income population" and "About 5.0% of families and 7.7% of the population were below the poverty line, including 9.5% of those under age 18 and 3.2% of those age 65 or over.":

http://en.wikipedia.org/wiki/Clayton,_Missouri

Also, I think that having a staff member positioned at the door explaining the payment procedure ("cheery employee Terri Barr greets everyone at the door and spells it out") and having employees watching you while you pay might deter long-term poor and homeless people from even stepping inside.

I went in there a few times. Most people actually overpaid a little bit, throwing in like a $10 when they got a coffee, main course, and a snack (this was 10 years ago, would've cost maybe $7 to $8 at the time normally).

Some people did take a meal and only put in $1 or whatever, but not too many and that's probably more than compensated by people who overpay a little. The key is probably where your location is.