Kim Stanley Robinson proposed a similar thing in his Mars trilogy... a habitat on Phobos used a train to provide artificial gravity. That was slightly simpler than your train, by virtue of only providing Martian gravity (0.38 gees), travelling at under 200m/s, only being ~60km long and only having to overcome Phobos' feeble half-milligee gravity, etc.
What are the flaws? How can it be made more realistic?
The largest one, perhaps obviously, is safety. Consider environmental safety. Building such a thing on the surface of an airless moon means you need radiation shielding, and quite a lot of it if you're expecting to shield against things like high-energy galactic cosmic rays. On Earth you're sitting underneath ten tonnes of atmosphere and a planet-sized magnetic field. On Ganymede, there's negligible protection from its atmosphere and feeble magnetic field and its proximity to Jupiter still provides a somewhat hostile radiation environment. Add to that the risk from meteorite impact, and you can see that the surface isn't a place you'd want to do this sort of construction.
Now, Ganymede is relatively low density, and its crust is expected to be both pretty thick and mostly made of ice. There's plenty of scope for building monstrous nuclear powered (presumably fusion, probably using deuterium mined from Ganymede) tunnelling machines to carve out deep subsurface spaces that are extremely well shielded from the hostile environment of the surface, and even well protected against all but the largest of impactors and those could presumably be tracked by astronomers and dealt with via various means.
This doesn't eliminate other safety hazards to do with the train hitting stuff, stuff falling off the train, etc, though if there's a roof over the tunnel you can at least avoid the issue of being able to shoot orbiting spacecraft using stuff thrown out of your much-faster-than-escape-velocity vehicle.
How practical is this approach compared to a regular space station?
Given Ganymede's surface gravity of 0.146 gees, in order to generate an apparent Earthlike gravity inside you need a centrifugal force of 1.146 gees... this manifests as a linear habitat speed of ~5.44km/s. A habitat in microgravity doesn't have this issue, but even if it had the same radius as Ganymede (a fearsome engineering exercise) it would still have a linear speed at the rim of 5.08km/s. Any debris impacts have the potential to be catastrophic, so you'd need substantial armoring in either case.
Now, the strength of the centrifugal force is proportional to the square of the angular velocity and the strength of the coriolis force is merely proportional to the angular velocity. If you half the radius of rotation whilst keeping artificial gravity levels the same, your angular velocity (and hence the strength of coriolis effects) goes up by a factor of $\sqrt 2$ and your linear velocity at the rim goes down by the same factor (increasing fall and impact safety).
Project Rho, as always, has some good material on the subject of coriolis effects, including this nice diagram:

You can see that the "comfort zone" (as derived from a bunch of papers, but no actual in-space experience yet) extends down to quite small radii. You don't need something as big as Ganymede to stop people suffering from coriolis effects like nausea and dizzyness.
Of course, in a small habitat coriolis effects will be a lot stronger than your Ganymede-sized track. A useful blog post on oikofuge.com gives a formula for the horizontal deflection of $d$ an object dropped from radius $r$ to radius $R$ in a rotating reference frame: $$d = R\left [ \sqrt{\left ( \frac{R^2}{r^2} - 1 \right )} - \arccos \left ( \frac{r}{R} \right ) \right ]$$ which is conveniently unaffected by the actual rotation rate of the object. I won't derive it for you here, but it is correct and only needs pretty simple trigonometry to prove it to yourself. You can see that for a 2km radius station, an object dropped from 2m to the floor gets a ~6cm deflection to anti-spinwards whereas on your Ganymede train it would only get a deflection of ~1.6mm which is basically negligible for humans. How much you care about this is up to you. From the point of view of story-telling or game-playing flavor, coriolis forces can add all sorts of interesting effects, IMHO.
Anyway. It might actually make a lot more sense to build hollow rock- or ice-clad habitats from asteroids, moonlets or ring material, with sufficient exterior thickness to protect against impacts and radiation. It is hard to judge the relative complexity of the engineering projects, but at the point where you're considering making multiple 5+ km/s, 16000 km-long train tracks (the other kind of rail gun) it doesn't seem implausible that you could make a bunch of 1-2km radius space habitats of this kind, and they be not just simpler than your circum-ganymedean train but safer, too... the outside rim of a 2km radius habitat is only going at 140m/s, and so is somewhat less vulnerable to impacts, and things flung off will be slightly more easy to retrieve.
Speaking of which,
And lastly, around the rings could be a carbon fiber mesh that could catch runaway equipment if anything where to go wrong.
You don't "catch", you "attempt to minimize destructive effects of the impact and spallation". You'll be needing Whipple shields.