You are leaving out some important context. The ACLU statement against those alt-right protests came in the immediate aftermath of a similar rally in Charlotte

You are leaving out some important context. The ACLU statement against those alt-right protests came in the immediate aftermath of a similar rally in Charlottesville that resulted in violence and death. People have a right to protest whatever their political viewpoint. However they don't have a right to incite violence. The ACLU no longer believed that these protests would be peaceful so they came out against them. You can argue that the ACLU made the wrong decision because maybe they were misinformed about the nature of the protest and whether it would lead to violence. But the principle behind their decision seems clear and obvious. They will support peaceful free speech and not support speech which incites violence.