Actually I've noticed from my own runs with the beta that passengers transfering from one bus/train to another don't pay again, however I could see every NEW viehical they might pay, say Train -> Bus they would pay but not from train to train, etc. Just my two cents on that.
You're probably right. At this point whenever I look at a metro station which has more than 100 passengers I get a red mist that's nothing to do with the mood of the waiting passengers; I haven't tried to count the revenue generated by each train...
By the way, I'm going in completely the opposite direction to DJW here. I never let two lines share a platform face. If two lines meet, there are two stations and the passengers walk out of one and into the other. The critical path is the amount of time it takes to move passengers from platform onto train, and sharing the platform with other line's trains doesn't help and isn't worth the cost saving of only building and maintaining one station!
A few thoughts on subways (which are driving me mad!):
Subways are the main source of income (because the tickets are more expensive, journeys are quicker, vehicles have highest capacity, and there's no delays from road congestion - each of those individually makes metro superior to tram/bus). When the subways get congested, the income stops, and so does the game. I'm paying maintenance on trains that are queued up in a tunnel, when they should be flowing and earning revenue. At the same time my bus and tram lines suffer because all their passengers are stuck at the back of a 500-CiMfolk queue miles away. I think it is critical that metros should work for the game to be completely enjoyable, so:
1)
Metros should not wait for passengers who've just arrived on the platform! They should not wait at all. Only passengers who are ready to board the train when it arrives should be expected to board. (It is worth waiting for last-second CiMfolk for buses and trams because they run less frequently.) This bug creates a Maddening Drip-Feed situation where the train is always waiting for just one more passenger until it is full. This is terrible for many reasons: it is the slowest way to fill a train. The train is full when it reaches the next stop, which becomes congested. If I add more trains, they just get stuck behind the one waiting in the Drip-Feed station, then they get Drip-Fed in turn, and Cities in Motion becomes Air Raid Shelter Tycoon.
2)
There seems to be something weird about how people queue for trains. There's 500 people waiting in the station. A full train arrives, 50 people get off, 40 people get on, then the train and crowd ignore one another while ten more people leisurely stroll on board. I suspect (but haven't been able to check) that the passengers have formed a very exact queue and they're all being very polite. And, also, they know how many people can fit in each carriage and where there's space left for them on the train. So, when the train arrives, instead of the 50 people nearest the doors getting on, the 50 people who've been waiting longest (and who could be standing anywhere on the platform) get on, and this involves an infuriating amount of Waiting for Mr Zimmer Frame.
(I am an English bus driver, and this infuriates me in real life too - when boarding passengers are politely inviting whoever is standing furthest from the door to board the bus first, when there is in fact enough seats for all of them, it makes no difference what order they board, they're just pointlessly delaying an already-late bus...aargh. I've only spent one day on continental Europe, but isn't the stereotype that there's no such thing as a queue over there? That would help CiM - and real-world public transport - enormously

)
3)
Passengers don't check if trains on other Lines will serve their destination. Suppose I build a subway across the city centre and out into a suburb. Suppose the suburban station is a Drip-Feed station. What I do right now is build two Lines on that one Subway - a Shuttle Line that goes from the Drip-Feed station to one platform of the next station, and a Main Line that goes from the other platform to all the rest of the stations. This way, only one train is held up by the Drip-Feed, but there's delay while passengers get off one train, walk around the platform, and get on the other. But the better solution would be to have one line serving all stations, and another just serving the busiest stations. Then the number of trains on each route can be adjusted as needed depending on where the queues are. This doesn't work, though, because the passengers decide which Line to use before starting their journey and would rather stand at the back of a 500-person queue than change their minds!
4)
Passengers don't recognise the hopelessness of their situation. If I decided to take the train somewhere, got the bus to the train station, saw a queue of ten train-loads of people spilling from the platform, through the staircase and booking hall, and out into the street, I'd recognise I'd be better off on foot, taxi, or hot air balloon. CiMfolk don't seem to be that aware!
But the root of the problem is number 1: metros waiting when they should be leaving. It is a bad bug, and it is amplifying the other three. Because of it, I can't just add more trains to a line to carry more passengers, because I just end up with an expensive queue. Of course it should not be possible to indefinitely increase a subway's capacity just by buying trains, but the limiting factors should be train capacity, speed, minimum headway etc, not by dimwitted overly-polite train dispatchers!
Everything else about the game is absolutely lovely, by the way.