My guess is that if you could poll big bank customers and ask them why they chose that bank, many would tell you they didn't choose that bank. Rather, it became their bank by way of a buyout of their smaller regional bank. As we all know, changing banks can be a pain, so I suspect most just eat as much crap as they can stomach from the big banks before they decide they've had enough and switch to a different bank (which likely will soon be swallowed up by a big bank - maybe even the same bank they just left - leaving them back at square one).
Small banks/credit unions for me, all the way. Thankfully, this is one of a dwindling number of industries in which there is still some level of competition (read hope for consumers). Hopefully, the big banks will continue to piss off enough customers to keep smaller banks alive.
As regards this story in particular, my limited understanding is that Visa is the big bad guy in the debit card fee fiasco. They own something over 60% of the market share, so they more or less make the rules. Being a big, profit-motivated corporation, they tend to make rules that hurt both consumers and retailers alike.
There is some reference to an effort in Washington to place strict limits on debit transaction fees in the article Marty posted. I had heard mutterings about this effort while managing a recent project wherein we implemented an online payment system. We did a feasibility study (sadly after the project had already been approved and initiated) to determine whether or not we should accept credit card payments. We found that, thanks in large part to Visa's abusive policies, we actually stood to lose large sums of revenue on some of our larger transactions, so we decided not to accept credit card payments. Those of you who use online payment systems will understand how much less valuable this exclusion made our project. Apparently, more and more businesses and institutions are refusing to accept credit card payments for this very reason. One example that I found particularly interesting was that this is why Washington State University does not accept tuition payments by credit card.