A necessary part of a free market is that consumers have choice. In the franchised UK rail system, there are very few routes on which one can choose between different suppliers. The franchise system also imposes huge barriers to new entrants to the market. Therefore, there is little incentive for companies, having won the franchise, to improve the service more than the minimum necessary.
The core infrastructure of the UK rail network is still owned and run by Network Rail, which is publicly owned, so the core inefficiencies remain.