Hillsdale College is the only college that refuses to accept any federal aid, even indirectly for this very reason. So the ACLU is being disingenuous when it fails to support free speech on private universities.
Not quite. Private institutions, even ones that indirectly receive federal funds, are not constitutionally prohibited from restricting speech rights on campus (and, for that matter, 4th amendment rights, due process rights, things like that). There are certain statutory restrictions (in things like hiring, discrimination, etc) that can be tied to federal funding (and so, Congress could theoretically pass a law applying free speech rights on campus), but there is no constitutionally protected right to free speech on a private campus.
That's not to say that it's a good idea for private institutions to restrict free speech (I think it's terrible). Only that it's not technically a constitutional/"civil liberties" issue, and so it's outside of the scope of ACLU activities.