Hmmm... what is the difference between the ACLU and a Libertarian? Most of the libertarians I have spoken w/ would not agree with most of the things the ACLU does.
It depends on the topic:
Abortion? None (although a few will say States rights)!
Special rights for Homosexuals? None!
Pornography? None!
School prayer? None!
Public commemoration of the Ten Commandments? None!
Gun rights? Oops! Bit of a difference there, for sure.
Enforcement of the 10th Amendment? Uhhhhh, hmmmmmmmmmmmm.
Federal income tax? Don't even get them started.
Like I said, it depends.