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.
I would like to see you cite court cases that agree with what you say FreedomFighter78. The assertion you make is popularly accepted, especially in Libertarian circles, but I am not aware that the Supremes decided that a private college that accepts federal funds may ignore or contradict Constitutional rights.
But assuming for a moment that you are correct, the ACLU is not an organization that simply follows precedent, it helps create precedent. Roe vs. Wade (for example) established a precedent based on premises that even most legal scholars consider ridiculous. The court position that a prayer by school students was an impermissible establishment of religion was precedent setting. The list of ACLU precedents is virtually endless. To suggest, as you do, that the ACLU would not find a reason to defend free speech in an institution that had part of its budget paid for by the federal government simply because of precedent is ludicrous.
And finally, to suggest that free speech is not a constitutional/civil liberties issue is so far off that you may not have been thinking when you wrote it.