I think you're pretty lucky if you've got an uncongested commute. For most places where people live a "driving" distance from work it generally gets pretty congested during rush hour.

For covering the benefits of a car, transit has some of its own benefits (mostly health benefits, but done right, travel time can be shorter), but I'll go through why losing the benefits you've listed don't worry me too much:

Direct line that can change route if necessary: my house and work are both close enough to transit stops that I essentially have a direct line from home to office. I'm not changing my route that often, but if I needed to get something on the way I'd rather just hop off and back on than have to find somewhere to park.

Ability to run late: I'll mostly agree with you here in some cases, but the key is frequency. Missing a train and having to wait an hour for the next one sucks, but I've never thought about "missing" a subway, the next one will be there in like 2 mins. If you have to look at a schedule for transit, it's doing a bad job. You should just show up and get whisked away in the next couple minutes when done right.

Strangers: fair, I don't mind much, but if an issue for you then it's an issue for you

Transporting things: The biggest thing I'm generally transporting is groceries, and I've never had a problem putting them on a bus (or more recently in my bike panniers, I was shocked at how much stuff you can fit in a pannier). But I also know a guy who brought a rowing machine home on transit, so if there's a will there's a way.

No interconnecting travel: I think this is only an issue if the connections are infrequent or badly timed. The same issue with "running late". When I hop off a subway and get on another line at the same station I barely even think about it. And I almost think of this one as a benefit, walking to and from stops and at transfers is free exercise. Take enough transit and you'll never have to use a treadmill in your life.

Multipurpose: I'll give you mobile locker, that's pretty nice (a bit expensive for my taste though). I think this goes back to the "stranger" point. I think shelters, benches, and lunch rooms should be public places. A public bench does a lot more good than a parking spot in my opinion.

While I agree there's no way to get everyone out of their cars and onto public transit (short of banning cars), the goal is just to make it a viable alternative. Even as someone who would just rather drive, if public transit is fast, frequent, and reliable enough, other people might be convinced which reduces traffic for you