It was called the Major League Baseball All Century Team, so if were going by that criteria, then we cannot include Negro Leaguers, even if some of them were all time greats themselves.
Since this was for Major League Baseball, regretfully Negro Leaguers must be excluded, since the Negro Leagues werent considered the Major Leagues at the time until just recently when Negro League stats got counted with Major League stats.
Honus Wagner was a panel selection. Keep in mind, racism is associated with Ty Cobb, but nobody discounts him as a top five player of all time (or even higher). Yount is a worthy Hall of Famer, and you have to be great if you had 3,000 hits and an MVP at two different positions, but Ripken scores higher sabermetrically, too, though Yount is closer than given credit for. The Iron Man streak is a big part of Ripkens legacy and perception.
Brooks was obviously a special defender, though historically, it seems Schmidt and a combination of Mathews/Brett are top two rankings-wise.
My opinion is Rose belongs in Cooperstown (one of the very, very, very few things I agree with the current White House occupant on), but All-Century, I feel others need their due justice.