Public transportation in the aftermath of an assassination attempt

I'm not sure what you mean. Can they stop specific trains/subways in response to specific information? Absolutely. I was on the Capitol Limited when it got stopped because of a suspicious package. And I've ridden the Late for Sure Limited (called by Amtrak the Lake Shore Limited) and dealt with the delays ICE cause every night. Commuter rail gets stopped all the time for various reasons.

Would they shut down the entire system? They could, and if there was a credible reason to do so, would. But just cause? Probably not. But they might induce some delays to get police officers to specific areas to scan the crowds.

Best of luck,

Jim Clark-Dawe

They would have an easier time shutting dow subways than buses.
I think about the aftermath of 911. I was in a doctor's office right after it happened and there was a tiny tv reporting the events. All the workers were calling loved ones, telling them to get home, making plans to go home ASAP. There was panic in the suburbs of Philly, a hundred miles from NYC and about the same from the pentagon. I can only imagine all the people flooding the streets in new york, trying to get home. Your scenario would be on a smaller scale, but if there were tens of thousands of people in a crowd where the prez was speaking, I can imagine chaos as folks rushed toward safety and to get home. Not sure if your setting is a sitting, but if so lots of folks would be heading toward public transportation, fighting to get on buses, squishing into subways. Even if there was a quick alert to bus drivers and train operators. It would be difficult, if he made a fast getaway, to alert them fast enough.

But on the other hand, every flight over the US or headed to the US was stopped at 10:31 AM on September 11, 2001. It was called a nationwide ground stop. Every plane about to take off was stopped. All flights in the air were told to land immediately at the nearest airport. (In some cases giant jets were landing at tiny airports in out-of-the-way places.) International flights were turned away and many landed in Canada.

http://wiki.answers.com/Q/How_long_were_planes_grounded_after_911

An assassination would prob. not trigger such an event (again) unless it was accompanied by some sort of huge (terrorist) attack, or the imminent threat of one.

But the ground stop was huge; it was possible, and it happened.

Your question was, "Can they shut it down". The answer is hell yes. The next question is, would they. The answer is, probably not the entire network, rather they'd set a trap at the terminal point. If they had critical intel an assassin was on a particular sub element of the infrastructure, they have data sources to establish the probable link or airplane or roadway, Saw it happen one time on assignment for the govy.