Jira also has momentum. I've advised at least a dozen places on, or moving to Jira (I was in for a different project but watched it). The reasons I heard were: new CTO had it at the old place, waits it here; and everyone uses it. Many of those startups also didn't have a Jira expert and soon got tangled in workflow automation that mostly got in the way for small, growth phase companies.
Accounting for the use of Jira is easy: known quantity and name recognition. A better question is "With so many unhappy customers, how do we still account for the continued use of Jira as an org matures?" It's the same answer but with the additional caveat that learning a new tool that's so fundamental is disruptive. I consult and advise multiple orgs and have done so for years. I don't often encounter heavy supporters of atlassian products, despite the number of users. Jira is one of those things that flies in the face of most UX logic in that it doesn't appear to lose market share, no matter how much slower, unreliable, inflexible and generally unliked it is. It seems that once a founder has grabbed the first thing off the shelf, you're stuck.
Full disclosure: I have no competitive interests in this space, I just hate garbage tools. (Apologies to my actual friends who work at atlassian. Your software is terrible.)
So full disclosure, I recently (literally this week) started a role at Atlassian, but not on Jira. Standard disclosure - this is 100% my personal opinion and not that of Atlassian in any way.
I think the thing that sets Jira apart is process management. It's the feature that no other competing tool really has to anywhere near the same level of power. If you're at a big org, especially one that has regulatory obligations, the level of control Jira gives you over workflows is pretty unmatched and it allows you to enforce certain practises and processes into the ways your teams work that mean that when you get audited, you can point to your Jira workflow and be like "See, we have system enforced process controls".
I also think that the Jira UX is... weirdly nice (personal opinion), in a brutal utilitarian way. If you compare it to some of the startups that are trying to disrupt Jira (I'm looking at you, Clickup), the UI is SIGNIFICANTLY less noisy.
Big ClickUp user and I feel you comment about it. It has become a massive UX mess. They really need to clean it up per "use case" or have toggles for users to disable UX features.
Too much is too much, and it's getting close to being too much on ClickUp.
But one of the killer features (IMO) is the fact that you can customise the flow of issues to match a flowchart. "TODO - IN PROGRESS - DONE" only goes so far when the org gets bigger.
This way it's a lot harder to move issues to the wrong state and the workflow is clear for everyone.
Jira offers them much more in the way of process management, reporting, and integrations with the likes of ZenDesk for its complexity. They seem to think of GitHub as just for the coders and aren't comfortable there.