There's nothing wrong per se in just sitting down next to someone, but it's friendlier and more polite to check first that the seat isn't taken. I suppose in the end it just boils down to what type of person you are!
I think it also depends on the type of train you are on.
For example on Merseyrail trains, there are no toilets, no buffet car or anything like that, so basically if a seat is empty then you can safely assume that it isn't taken. In fact it would seem unusual on such a service for someone to ask if a seat is taken, it virtually never happens. It's just like being on a bus or something.
Conversely, on longer distance services, on trains where there are toilets, buffet cars etc.. then I agree it's not a bad thing to ask if a seat is taken or not. If I can make eye contact with the occupant of the seat near the window then I may ask. If they have headphones on or are ignoring the world around them, looking out out of the window, then I may not ask. When people plonk themsleves down next to me without asking, I am not bothered in the slightest. I am quite used to it and I always ensure the ailse seat is available and none of my stuff encroaches on it.