Honestly?
Car parks.
Car parks rake in a fortune for the rail business. The more people that drive to the station, the better. Even if they don't park there, they will be parking at nearby (and substantially more expensive) local government owned/franchised parking arenas therefore generating more revenue.
Once out of the car, the person (singular) occupying them takes up minimal space on the train, at maximum income, irregardless of train fare. In addition, footfall off the train can be forecasted. Should there be an upsurge in car/foot passengers there isn't a major problem, as there is always additional space for those willing to stand or be pressed against someone's armpit.
Contrast with bike. No revenue from parking charges. Cyclists inherently take up additional space on train which is unable to be utilised without the presence of cyclists and therefore increase costs directly to the business. Bikes slow traffic onto the trains because, frankly, they're not built to accommodate them... therefore they also slow traffic off the train, which means it gets further delayed.
Should there be a sudden unforeseen upturn in cycle passengers there is an exponential growth in the amount of space required, and time required at each station. We get in people's way be, as above, trains are not built for us.
Bikes throw a spanner in the works quite spectacularly. Frankly, if I were looking after a train franchise, I'd hate us too.