I'm sure they will be fine. Mine are a similar age and regularly travel Leeds to Peterborough to school on the train. Some things we did were:
Get a platform ticket if the station is a closed one- costs 10p you just buy them at the ticket desk. You can then meet the kids on the platform so don't need to worry about where to meet up/ put them in the train so you can find seats
Make sure one has a mobile phone you can track- find my friends in iPhone for example- and ring them 10 minutes before they need to get off.
Book first class- it's not much more for child tickets but it's less likely to be crowded and you get free snacks!
We've only had two problems with the train- one where it had to divert to go round a broken down train and ended up being half an hour late, and one where the train was cancelled, DS1 was 12 and just text me to say 'train cancelled pick me up at York'- he'd seen the departures board, gone to the ticket desk, heard the person in the queue ahead of him being told to get on any train north, and worked out the next train would go to York, which was close enough! He could have changed trains of course but it was easy enough for me to divert.
These days with the internet and mobiles they are rarely entirely alone, they know they can ring you for advise or look up what to do online. They will see it as an adventure!