The anti-trust action against them did not cost them a lot of cash directly, but it did lead to heightened scrutiny on further anti-competitive practices. And it wasn't too long after that the FAANGs came to displace Microsoft as the dominant technology companies.
Could be a coincidence, but I personally feel like there was a connection.
Imagine a world where IE6 never has to compete against Firefox because every version of Firefox is mysteriously "broken" by the latest windows update. "DOS ain't done till Lotus won't run" for the late 90's early 2000s. I think that its a very realistic thing to think that anti-trust played a huge part in allowing the open web to flourish as it, even with MS fighting as hard as it could to stall it out with IE stagnation.
They became victim to the same corporate diseases that plague all public companies after a while.