Market share isn't a valid excuse for a bank. Through fees and the interest rate of my Chase credit card, I have probably just about paid for the cost of the Windows Phone app. A bank is about convenience to the customer. It's bad enough when someone won't develop for Windows Phone, it's a whole other issue when they choose to end support for their existing app. I fully expect to have my Chase card paid off so I can close my account before the app is officially turned off.
It's more than just user base; it's ROI. Any good business considers it. If it's worth it, go for it. If it isn't, don't. It's quite simple in theory. Chase & BoA know how many WP users use their app, and they probably have a good estimate of how many will leave their bank because of it. It's a calculation based on educated guesses.
I hate to break it to you, but the ones making the call are probably better at making those decisions than you or anyone else here would be. The bean counters have their jobs because they're good at what they do. I would venture to say they know what they're doing, in spite of your skepticism.