I'd go a step further.. The prof was expressing empathy for the students that made the effort to be on time. They made it.
If you know you're late all the time, then make allowances. 8 hours not enough sleep, go to bed earlier. 1 hour not enough time to wake up, set your alarm to give you 2 hours.
This isn't related to knowing you're sick, just knowing you're late often.
It always makes me wonder when I hear "empathy, tolerance, flexibility" pointed at a group of 30 or more, who need to work around one persons inability to do the same.
I had a co-worker who was always late. I told her she was lying when she said she'd be there at 2. She got miffed. I replied. "You're late so often, do you expect you'll be on time. I know you'll try, but do you really believe you're not going to be late." She paused. "If you know you're very likely going to be late and tell me you will be somewhere at time X, then you are lying."