To give another data point: in France I remember the university having to ask the local profs. to put their titles (Dr, Prof, etc) in their mail signature as otherwise students thought that french teachers were much less competent than e.g. teachers from germany who would have three layers of Dr. Eng. prepended
One common situation is introducing an invited speaker at a conference. After the first mention, you refer to the speaker using a mix of pronouns and names. Full name or last name would sound weird. Using first name works if the speaker is your friend and many people in the audience also know them as a person. Otherwise "Dr. Lastname" is a reasonable choice.
Academic websites are full of short biographies of speakers, lecturers, PIs, and so on. They are often written in third person. Again, "Dr. Lastname" is often the form of reference that sounds least weird.
Academic spam is often addressed to "Dr. Lastname", especially if the sender is asking the recipient to do something. Using "doctor" as a title is a safe default choice. It sounds respectful, it's very likely to be correct, and it saves the sender from guessing the gender (and possibly marital status) of the recipient.
A PhD has earned their title "Dr".
Many people use it, and they should. They paid for it with their mental health.
I apply the title to everyone I know with a PhD.
Perhaps the PhD holders don't want to be associated with the hubris that most medical doctors exude. For reference, google "endometriosis suffer" or spend some time researching medical malpractice.
It also is possible that a lot of kids coming out of the 80s got a bum deal on their education - or at least feel they did. Like, "it was too easy to get this degree" - from the standpoint of applying themselves, not the overall workload of getting a PhD. Medical Doctors who are board certified, that did all their rotations, and whatever else required, there's only one other doctorate that requires more workload, and that's psychiatry.
What should maybe be questioned is why someone needs a doctorate for "the world to learn from them."
Granted, these are mostly (or even all?) people who received their doctorates in the past 10 or 15 years, and as such are a good 30 years younger than Stallman, so perhaps there is a generational thing at play here too, where the respect/desirability of titles like that has been dropping over time.