It's not "fuck you"; it's not, "stop being a crybaby snowflake"; it's not, "you are a sinner who will burn in hell". It's it's a term used to unenthusiastically express assent, agreement, or acceptance.
The entitlement is so strong that even passive acceptance is unacceptable. Anger at "ok boomer" is anger over someone who is exhausted and walking away after they've been punched one too many times because the person punching them wants them to keep fighting back because they enjoy the fight.
I find it really hilarious when Gen Xers especially (and sometimes Millennials) get real upset about "Ok, Boomer"'d and go on a rant about how they're not a Boomer...
Like, what a wonderful way to illustrate you are a Boomer in your soul.