Speed, space, and cost usually. With busses it is way faster to board if you can just open all the doors at a busy stop and everyone paid on the platform or online. They just get on and sit down and go. The busses in Chicago let you pay by credit card (tap) to get on, which is not particularly common in the US, which helps with this.
It’s also much more expensive and challenging to build a system separated by fare and non fare zone. CTA runs a very old system that was designed ages ago so its pretty easy to keep it that way. Many newly built systems are dealing with expensive right of way acquisition and high construction cost. It’s way easier just to slap a few pay stations around and call it a day. Most people pay to ride voluntarily anyway, and those that can’t afford it weren’t going to pay if there was a fence in the way.
Source: enthusiastic about public transit and city politics, feel free to correct me please