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I've just started using the activity editor, and I put together a simple passenger activity on the NEC. With this activity MSTS is immune to comfort level violations. You can put the train into emergency and the activity evaluation still says "Passenger comfort levels were maintained." Normally MSTS is sort of picky about this. Is this something you can edit in the activity editor? Is it related to the consist you pick? I've seem some consists that are labeled as "durable" or "fragile".
The Passenger Comfort levels seem to be related to the difficulty level. The 'Easy' level is, as you've found, almost immune to passenger comfort, while at the 'Hard' setting it is all but impossible not to jostle the passengers.
I think it is the consist. When you make a consist, it has a durability rating shown as a factor of acceleration in the form __m/s/s, with a guide of what is durable and what is fragile. A note, for comparison, the acceleration due to gravity is 9.8 m/s/s. If you have ever skydived, that is your acceleration when air resistance is ignored. The difficulty is actually just a comparative rating given by the designer of the Activity. The same Activity could be labeled "Easy" or "Hard", and have no differences at all.