Do people use their metro cards only on the subway? How common is that? The one thing to keep in mind is that a metro card acts as payment for all of these modes of public transportation:
MTA Staten Island Railway
MTA Bus Company
All PATH stations
JFK-AirTrain
Westchester Bee Line Buses
Roosevelt Island Tram
NICE Bus (Nassau Inter-County Express)
You can't really say that the MTA is out to steal money from you or hiding how to optimize your top ups, because not all of these cost an even $2.50, and MTA doesn't even set prices on all of these. Maybe you can write it off as paying for convenience, but the 5% bonus adds up since cards can last over a year. You only really have to worry about the amount on your card the last time you top up.
Even if you only take the subway, if you put at least $50 on the card, you're playing with house money including the bonus. A group of tourists can easily reach this over a four day weekend.
> you're playing with house money including the bonus
No, you are never doing this. The prices should just be 5% cheaper and there should be no 'bonus'. The fare is obviously set taking the bonus into account, so it makes more sense to just drop the prices and to drop the bonus.
There's more to it than that. MTA is competing with, for example the port authority's SmartLink cards when it comes to paying fares for the PATH trains. That 5% bonus is also a carrot to get people to get the metrocard.
Even if you only take the subway, if you put at least $50 on the card, you're playing with house money including the bonus. A group of tourists can easily reach this over a four day weekend.