The rules appear to prohibit singing or playing of an instrument without a permit. No mention of religion that I can see. What if she were singing the Internationale or some rap tune?
Reasonable restriction for those riding on public transportation. As to the manner of her being escorted, that’s another issue worth examining, but the Article 1 claim is bogus.
As I posted the State’s Constitution says “There shall be no law [...] penalizing the free exercise thereof” — this law does indeed penalize that exercise [as shown by its application in this instance] and therefore (this case, at least) should be found nullity — granted there could be a better way to phrase the constitutional language (as in NM’s Constitution) with “no law shall abridge [...]”.