I would worry more about the train - flights are far more controlled.
I travelled to Newcastle from Aberdeen at 15, having never travelled further than 3 miles alone. I took the Friday train at I think 3, maybe 4 and by Edinburgh most people on my carriage were drunk. One man I can remember was with several friends, all looked 40s/50s, sat across the aisle and started asking me where I was headed. Landed up with transport police meeting him due to his later actions with another woman.
Awful journey - the lights went out completely on Forth rail as well which was scary (mid February, train in pitch black suddenly) and had a very heavy period.
I won't mention the fact that my very liberal aunty met me with a bacardi breezer!
It depends of course where they are going/when but if it's heading towards Glasgow, Newcastle and probably London I would reckon there will be drunk people, more so on Fridays and Saturdays.
On weekdays, Sundays, early mornings, I've never had a problem. Similarly, going north has always been fine as well (i.e. Edinburgh to Aberdeen/Inverness/Wick lines). I presume similar happens down south.
So train wise, I would book very wisely and tell the staff once they board the train. As boys there's probably far less risk of problems like I mentioned but they might still feel uncomfy with regards to atmosphere at times.
Would get them to take a phone, spare cash, list of stops and an idea of what to do if they have to disembark at each one. Also have them keep their bags with them, under the seat or something.