I thought the idea was to transport as many people as possible? So what's the problem with a lot of people at every stop. Isn't that what you want? Good network transports a lot of people... bad network barely has anyone using it.
But even Berlin, the largest city, has only 30,000 people living in it, so it's reasonable for a subway train to only hold 40, or for a bus to hold only 10, and so on.
If the vehicles have "realistic" capacities, that overloaded station with 300 people will be emptied, yes, but then there will be no one for the next train to pick up. You'll have one very profitiable vehicle and the rest will carry 1-2 passengers at a time.
If your stations are overloaded, it's due to the layout and number of lines. When I build an initial subway line, let's say, across Berlin, west to east, going from the Stadium to Alexanderplatz, it's going to quickly become overloaded, especially in at the stations in the city centre. Someone going from Tiergarten to Alexanderplatz is going to use the same line someone going from similar points north of the Spree.
However, if I build another line north of the Spree, paralleling the first, the amount of traffic on the first is going to drop because all of those north-Spree people are taking the second line now, instead of the first.
That's why, in the Berlin map, I tend to build my lines in a grid, alternating between north-south and east-west.
Crazy, but realisitic.
I'm guessing that all those unhappy people are from breakdowns, right?