Because if CD Baby was acting as a middleman and a gateway for indie music distribution, Apple's move to shut it out was about preventing power from becoming decentralized and keeping control concentrated in Apple's hands to position iTunes as a premium platform. On top of that, if CD Baby had monopolized the indie music market, any future platform would only need to deal with CD Baby, which would have been a burden down the line.
It was likely a strategy to capture the entire music market. Sometimes I wonder why people don't get as angry at Apple as they do at Microsoft. I don't know what the image is like in the US. Personally, I've always thought Apple's premium strategy is terrible