Not that homeland insecurity has any (or many) compunctions about constitutional and other fundamental American philosophies towards gubmint services, but here goes:

The reason is that there is nothing illegal about it. There is no federal interest in queue management for how folks get in line to be subjected to and suffer TSA's security theatrics as long as access to the gubmint's theatrics is not discriminatory based on any of the prohibited criteria (race, ethnicity, sex, preferred pronoun of the day, etc.) and results in disparate impact. In this case, the gubmint's services are still equally provided to all - one simply doesn't have to wait as long. The clear service is materially no different than some airlines providing expedited access to the theatrics to their first class pax. So, TSA cannot not allow this commercial transaction between the airport & airline management and Clear.

The other major factor is that Congress specifically encourages companies such as Clear Secure to develop the technologies to provide these products and services as the primary aim of the SAFETY Act https://www.safetyact.gov/ to help make us "safer." So, don't blame TSA, blame our congresscritter overlords.....who, you know, are just doing it for us.

In answer to some of your other questions: yes, airlines and airport operators share in the costs to operate VIP lines - which is why such lines are so few and far between. In addition, they are even more scarce since now Clear pays the airports to essentially provide this service.