It is the American Civil Liberties Union, Not the Union of Americans' Civil Liberties. 'American' in this context refers to the provenance of the civil liberties in question, not some sort of property interest. The more you know!
If American liberties are a concept to apply over the whole world, the ACLU should be encouraging the whole world to a adopt the Bill of Rights and our Constitution.
Isn't it reasonable that we should seek to limit the actions of our government towards non citizens to those actions that are necessary or beneficial (either to US interests or to both parties)?
So for example, it may be reasonable to investigate the backgrounds of people that would like to visit the United States. But after such a reasonable investigation, I personally don't think the government should then be allowed to use those people as political props.
Our Constitution contemplates the arrival of immigrants and indeed specifies that their should be 'uniform rules' for their naturalization. It also distinguishes between citizens and persons, granting some rights to the latter group and limiting others to the former.