Because the city sold them on the basis that they offered an exclusive right to pick up street hails in manhattan. Uber, et al, have essentially eliminated that exclusivity.
They sure did. I used to have three numbers of black car services on my phone, and if I couldn't get a cab, which was common in my neighborhood, and I needed a ride badly enough to pay 2-3x what a yellow would cost, I'd call those numbers one by one, until one of 'em had a driver available. If I was in manhattan, I'd pretty much never call a car, because it was easier to street hail a yellow, usually.