We don’t want people to travel from highly infected areas (because they might be infected) to areas where the virus isn’t spreading (because that could bring it in).
Having someone with the virus traveling to an area where there’s already significant spread doesn’t really change anything. If you don’t have COVID-19, you won’t make other people sick. And with so few people on planes, social distancing is easy, the actual travel itself is fairly low risk for passengers – though higher risk for flight attendants.