The rough estimate of the amount of damage a tonne of CO2 released into the atmosphere causes is $196 (source: wikipedia).
A an economy class return flight from Munich to Barcelona (a typical night train distance) releases 0.45 tons of CO2 per passenger resulting in an additional cost of $88.2 (72.6€), 36.3€ per leg.
Every extra tonne of CO2 does cost $196+ (I’ve seen credible estimates as high as $400), but through offsetting you could verifiably ensure that more tonnes are avoided for far less.
As a crude analogy, if there is an oil spill (causing $$$ of damage), it would still be cost effective to plug the next oil spill for $.
Don’t get me wrong, the ideal scenario would be to not cause the first oil spill at all (in this crude analogy), but given that this seems impossible in our society, an offsetting tax on plane tickets could be a highly cost effective lever instead.