I suppose different trains have different layouts. So far I've always been able to sit immediately beside my bike or in direct line of sight (close enough to shout "OY!" if anyone's gaze lingers on it. :p) In any case, the bike itself is parked with front wheel in a rack or the whole frame is strapped in - depends on what facilities the train carriage has fitted.
I've never had any damage happen or any situation that made me think there was a risk of damage.
Maybe check out what bike facilities are on the rolling stock your train company uses, then decide if it worries you too much?