I haven't watched The Daily Show in a long time, so I don't have much of a horse in this race; but I could tell a lot of people were really hopeful that Roy Wood Jr would get the host role.
Hearing about the guest host roster and the entire process definitely is reminiscent of when Jeopardy short changed Levar Burton for the host position. It was later revealed to have been a play by the (former) executive producer to give himself the host position; but by the time Jeopardy got its house in order, Levar Burton had already been given his own show to host.
I think a lot of times studios aren't really as in touch with what people want as they think and they can easily overlook a crowd favorite. I'm hoping that similar to the Levar Burton Jeopardy situation, this will reveal Roy Wood Jr's popularity to allow him his own show as well.