Why is force dependent on acceleration, not velocity?

The $F$ in the equation $F=ma$ is not the force that would be exerted by the object if it were to hit something else. Instead, $F$ represents the net force acting on the object that must be present in order to produce the current acceleration $a$ of the object. A better way to write Newton's second law is $$F_\text{net}=ma,$$ since it shows explicitly which force is being represented on LHS of the equation is.

In your train example, if the train is traveling at a constant velocity of 100 mph, the acceleration is zero, and by Newton's second law the net force is also zero. But this has no bearing on what force the train would exert on something if it collided.