Lots of reasons. Here’s my take as a lifelong 4th generation resident of the Archdiocese of Chicago.
Cupich is a strong supporter of Pfleger. When Cupich came to the Archdiocese he made a point to visit Pfleger’s parish and state publicly “I’m here today to give you a word of encouragement but also to let you know how much I admire you, I depend on you.” and "Every parish should have the vibrancy of this parish.”
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Cardinal George made efforts to rein in Pfleger, but the threat of schism made him back down. In that case all the media support was on Pfleger’s side. After years as a media darling Fr. Pfleger had enough of a ‘power base’ to win in any public disagreement.
Bernadin (like Cupich) was a strong supporter of Pfleger and gave him support in all of his actions. That support and space allowed Pfleger to build up his power base with politicians and non Catholic local religious groups and other social/political organizations.
Pfleger always provides local media with great copy and content so they love him. In nearly every situation when there is any effort to disagree or rein in Pfleger the local media will report from the perspective that Pfleger is on the good side.
The community he has built at St. Sabina is not necessarily Catholic. If you look at the website you will find no mention of sacraments, no RCIA or ‘join the Catholic Church’. Many of the people who are active in the community (including leadership positions) there are not Catholic.
Cupich has removed priests for much less (much, much less) than inviting Farrakhan to speak in their church. My guess as a Chicagoan is that nothing will be done to Pfleger unless the media pressure becomes too strong to resist (something unlikely to happen as the media generally supports Pfleger).
The reason nothing will be done is that in this case Cupich will just wait it out and nothing will result.