At some point, the senate was afraid of gridlock, so there was a special provision made for things that deal with money (not sure if tax only), where things that have a minimal impact on the budget can overcome a filibuster with a simple majority. The parliamentarian is the one who decides if a bill is "minimal impact", which is set at $1.5T at the moment.
Therefore the parliamentarian has decided that changing the non-profit law would cause this tax bill to be more than $1.5T in net change, meaning it can be filibustered.
Edit: Wikipedia article [1] https://en.wikipedia.org/wiki/Parliamentarian_of_the_United_...
[2] * corrected my math, thanks to dragonwriter