> If the tax is enough to cover CO2 sequestration, where is the problem?
Social unrest, plain and simple. When the rich can continue their lives as usual and only the poors have to rein in their life style, there will eventually be riots. We're already seeing social unrest with the election results for the 45th in the US and the very near election of le Pen in France that runs on precisely this ideological framework.
Besides, we need to reduce the total CO2 emissions to keep the 2°C target, not just keeping the current emission amount.
> Why not the same exemption for sub 2-hour flights?
Same as above, plus the reduction in noise for the people living next to airports, and (more an issue in Europe) reduce the amount of space that is needed for airports. A high speed train is way more efficient in terms of energy, CO2 emissions and required staffing than an airplane is.