The implication is that if Trump is against everything the ACLU "stands for", the protections are anti-ACLU? This is categorically inaccurate.
We can parse the syntax more but my main point is simply that the ACLU has consistently stood for equal protection under the law. Trump is the new variable in this situation and brings a wildly anti equal protection view so he crashed into them (and the Constitution imo) not the other way around.
Frankly, I'm not convinced he has even read more than snippets of the bill of rights.