How can I protect against shorts in low voltage AC ~16V
If the short-circuit current of your transformer is less than 40A you could use a Polyfuse such as the Littlefuse 30R500UMR. They're cheap (under a dollar in singles), and automatically reset when the fault is removed.  



It needs to have a DC voltage rating of more than 22V, so this model is okay (30V rating). 

Here is the trip time curve for this series of parts: 



If the fault current can exceed 40A, it might not shut off reliably (and could damage the Polyfuse). You might want to put a somewhat higher current rating 5x20mm 250VAC fuse in series if you're not sure about this detail. It's possible to estimate the maximum fault current if you have the ability to measure the transformer secondary resistance accurately, but that's another question. 

Another option, probably the one I would choose, would be to use a thermal circuit breaker
such as the TE Connetivity W51-A122B1-5 or the W58-XB1A4A-5. Those items require manual reset, but have interrupting capacity in the 1000A range, which is not going to be a problem unless you are using a transformer sitting outside on a concrete pad for your train set.