It's less a matter of difficulty in crossing the atmospheric interface (boundary between space and not space), and more an issue of being in a useful orbit in the first place. If you're in a geostationary orbit, you're pretty far out and have to add the flight time to and from your launch point which burdens response time. If you're in low orbit you will be circling many times per day, which can put you severely out of place (wrong side of the planet) to respond to events. Matching velocities for orbit, calculating flight times, and managing fuel reserves all become much bigger concerns in trans-atmopshereic operations.