The British Association of Train Operators (ATOC) has issued a short guide to rail fares. I think it is worth restating here.
In response to the question, "Why do many fares rise every year?" they say,
"The overall level of fare rises is determined largely by Government
policy. Since 2004, the Government has sought to sustain investment
in the railways by reducing the amount that taxpayers contribute and
requiring passengers to pay a greater share."
They go on to say that successive governments have done this in two ways:
"1. Around half of all fares are linked by a Government formula to
July's inflation rate as measured by the retail price index (RPI). These
are known as regulated tickets and comprise Season tickets for most
commuter journeys and Off-Peak fares on most intercity journeys.
"2. Train companies set the remaining fares, known as unregulated
tickets, (such as intercity journeys at busier times of the day). These
cover journeys where passengers have choice about whether or not they
travel by train and so prices reflect market conditions.