I run a company that makes the urethane foam used in train seats (suspended graphite foam). I supply most if not all domestic train seat manufacturers/ refurbishers as well as some in Europe. Whilst it is true that I have to comply with some of the most demanding Fire, smoke & toxicity (FST) testing in the world (more rigorous than any aircraft, which I also supply) it is not the reason for hard or uncomfortable seats although it can be argued that there is some causal effect. The more foam in a seat, the more difficult to pass the fire tests but (generally) the more comfortable the seat. However, more foam means more money. That I'm afraid is the driver.
As the foams get thinner they have to be harder to prevent 'bottoming out' under compression so you have what we see detailed in the Times article.
I had the opportunity to address a working group put together by the Rail Safety Standards Board to discuss passenger comfort and how to attract people on to the railway and off the roads. I was vociferous in my condemnation of both the ever increasing passenger density and the poor comfort levels. I ended up pointing out that nothing would be done whilst the driving force was the cost of the seat. I repeated this at a follow up meeting where they were inviting tenders for funding to undertake a study in to rail comfort.
There are more comfortable seats available in the UK, although very few that are fully compliant with the latest crashworthiness standards but the TOC's / franchise holders do not want to pay for them. They'll take your £5K for a season ticket and the government subsidy but they have to maintain profits for their Dutch/German/French masters.
On behalf of the train seat manufacturers, you may be interested to know it cost over £750,000 to design, tool and test a new train seat (speculatively!) and then they have to ask themselves who are we designing for? Today's 50%ile male / female will not be tomorrows as weights and dimensions increase. I have my sympathies for what is a very risky enterprise.