Fans inside of the tube would pull air in the direction of travel, and it could be circulated or pumped in from / out to the outside at the ends. At the end of the tubes a main fan system would be the primary work horse, creating vacuum forces on the arrival end and pushing forces on the departure end.
In the last mile, the fan system could shut down and use the pressure to help stop the vehicle and even store some of the pressure to help start the system in the opposite direction later (i.e., regenerative breaking).