The “Freedom Riders” chose to target interstate buses for desegregation for two main reasons.
First, segregation on such buses was clearly illegal. The Supreme Court had ruled in Boynton v. Virginia that segregation in interstate transportation was unconstitutional. This was true of the buses and even of the bus stations in the various places where the buses stopped. Therefore, the activists knew that they clearly had the law on their side.
Second, interstate commerce is in the jurisdiction of the federal government. Things like the lunch counters where sit-ins had occurred were under local jurisdiction. But the buses were under federal jurisdiction meaning that incidents on the buses would force the hand of the federal government. The activists wanted to make sure the federal government had to get involved.