Glass is chosen because of it's chemical composition. Certain glass formulations are very close to the composition of bone, making it very biocompatable, and the composition can be tweaked for various behaviour (mostly regarding the way nearby tissue reacts).
Furthermore, you are far, far overestimating the issue of the capsule breaking. Any trauma sufficent to break the capsule will cause massive trauma, break or pulverize bones, and probably be a far greater issue. Basically, capsule failure of the glass tags is a non-issue from a medical standard.
A quick perusal of pub-med seems to support this, though it wasn't exhaustive. There is one interesting article looking at the survivability of RFID tags under extreme temperatures (such as autoclaving or liquid nitrogen), and only had one tag fail (and it didn't rupture or anything, it just stopped responding)after the tenth autoclaving cycle.
Basically, despite the fact that it's glass, implantable RFID tags are ridiculously durable, and far stronger then the puny human and/or pet they're normally implanted into.