I struggle to understand why you are so sure of this. Traveling by train is already far, far more popular than traveling by plane in most parts of the world, but you don't see security checks there.
Maybe if someone figures out how to slam a train into a skyscraper. This seems rather impractical though, as terrorist attacks go.
But that's what it took for air travel. Hijackings were even relatively common pre-9/11[1], and they didn't even bother to start locking the pilot cabin door (probably one of the only security measure implemented after 9/11 worth anything at all) until someone did something that extreme.
That's basically true for now, but if rail travel became much more popular I am sure that would change.