They planned their errand
That’s the problem if they didn’t consider the limitations. It’s a irrational expectation for the bus to be 100% efficient and always on time. Nothing is 100% efficient. It’d be a faulty expectation to assume that things (other than death, disease, aging, etc.) are certain or guaranteed.
not also deserve empathy?
Everyone deserves empathy. All sentient beings, including this hypothetical man.
Do all these other people not also deserve empathy?
Again, all people deserve empathy. It seems that you’re making this a binary, “either/or”, dilemma when I believe both the angry transit operator and the smoker are “not ideal”, though I do have a bias toward the anger because that is aesthetically uglier than the smoking.
The ideal is a very liberal one, tolerance of all views. I do think it begins to be a problem where tolerance in of itself is in conflict. There does need a “do not harm others” baseline before tolerance. For example, I just had a conversation the other day about “armed groups” where the other person was in favor of militarizing against oppression, which is an intolerant position (War and warmongering is intolerance.) If my opinion is that I want you dead, it’s not an opinion or a view but an incitement to violence.