Well, I'm not going to attempt to recover my statements from earlier as I just can't be @rsed to re-read the thread, recall what I meant and then rephrase BUT ... the question from Katamarino is easy to answer.
Because they can make more money.
You may know that the airline world uses a process called Yield Management, that is based on previous numbers that used a particular service and current demand. With each year that goes by, the system becomes more finely tuned.
The problem for us is that, we grew up knowing that busses and trains were flat fare and that aircraft were variable. After a lifetime of having this inculcated into national behaviour, it is highly disruptive to have train fares moved to variable.
Whilst I will always think carefully about taking a plane - due to the time and distance involved - I might just decide to take the train to London to go shopping, see a show or a friend. Now, I have to think twice. The more so when it is cheaper to go by car and if I take a passenger myself, then the cost benefit really moves in my favour.
However, it seems that the govt (both Labour and Conservative) want the train companies to make more money, so that they can reduce the amount of central subsidy. If only it worked that way ...