2 of my children take the train to their (different) schools, from SE London out against commuter traffic, so quite quiet. It's only 22 minutes, one train - but by the time they walk to the station and then on to school the other end, it's about an hour.
It has never bothered my son (now y11). My daughter really really minded it throughout y7 and 8, but is accustomed to it now.
The 'pluses': they are very independent. Some of my friends drive their 13 yr and 15 yr olds everywhere. Mine are pros on the Citymapper App, and can get themselves in and out of anywhere in London, and I am pleased to give them the little freedom and independence they have, compared to my teen years.
When things have gone wrong with the transport, it has been scary, but they managed. And learned, and it's not scary any more. And thank heaven for phones so I could direct them to alternative routes. And my eldest has the uber app, and they all piled into a cab 2 weeks ago (they are not ever allowed to get into a cab/ uber alone.)
They both like the time on the train: sometimes a little extra revision/ last minute homework time; mainly, a time to hang out with the many other school friends doing the commute. Their train friends are almost closer friends than their classmates.
Cons: the time. DD has clubs at lunchtime, DS had some after school, and would get back from rugby at 6pm. But he coped. The expense: I feel like I am constantly putting money on their zipcards...the bus would be free, but takes 90 minutes, not even door to door.
Overall: like all these things, think it is horses for courses. You 'll know your own child, and know the commute. Try it one day, at the times your child will need to travel and see what you think?
Good luck OP