Two bad reasons:

• If the system doesn’t get it’s money back, you can use that as justification to cut funding because it’s “not profitable”. Never mind that most city services aren’t…
• Police can use “lack of payment” as an excuse to kick poor people out of the system whenever they want. Transit systems tend to allow this under the belief that people who can pay the fare will refuse to ride with people who can’t, but anyone that snobbish won’t be on transit in the first place.

One less-bad reason:

• Systems can use fare payments to get data on routes: how often they’re used, at what times of day, etc. Metrics are important to justify your position in the city budget. Of course, there are other ways to do that which aren’t as harmful to poor riders.