This has been the trend for more than a decade now. AP is not only viewed as not rigorous enough by top colleges, but they do not want to lose the money by giving away all this credit and excusing people from taking classes and being there for a shorter period of time. Schools also want to be able to ensure an even, fair curriculum experience for all students, and many high schools do not and cannot have robust AP programs.
There is a key inconsistency happening at the selective schools here. As fenrir points out it's not uncommon for a selective school to require a 5 or even not grant credit at all. Yet they will often offer their own placement tests into sequential courses like math, science, and foreign language. Many of them will then offer credit for the prerequisite that was skipped upon completion of the later courses in the sequence.
Here's the twist. It's isn't that hard for a student who gets a 3 on the AP to get placement through the schools internal placement test. If they grant credit retroactively they have essentially done what AP designed the test to do - make a 3 equivalent to a C from a state university for purposes of transfer. The selective school has made themselves feel superior, but really haven't done anything different than simply accepting the AP score in the first place.