The statements of candidate Trump suggested a system far broader in scope than NSEERS to cover US citizens. The Kobach plan to reinstate NSEERS (it was halted in 2011) would presumably involve more invasive point of entry procedures for more countries.
Whichever way it is, the real time to stop NSEERS was when it started in 2002. Since that didn't happen, it didn't stop until 2011. So yes, it is a good time to complain about religious profiling when a new administration is planning to institute it.
The info about it is all available publicly.