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I don't intuitively see why trains would be massively cheaper than a circle nowhere interesting (underground).

HS2 is too expensive, sure, but the LHC is built next to ~a century of research institutions and took a very long time, whereas trains can actually be on somewhat tight schedules in the places where it actually matters and requiring bulldozing a fuckload of expensive land, houses, and history etc.

There are a lot more trains than particle accelerators, I'd think economies of scale would be significant

It's an electron bound state nevercollider.

And the protons go 3 million times faster than the trains.