Since it's subsidizing specific behavior and not merely being poor or whatever, people will naturally look at whether they think that behavior ought to be incentivized, or whether the government should stay neutral.
My wife is also a stay at home mom, and I've argued before that an increase in the child tax credit with a phase out for high income (so we might not qualify) makes more sense than a childcare credit/deduction for this reason. Then you're just subsidizing having kids, which seems fine to me (assuming we're subsidizing anything) since that's sort of necessary to sustain society.