The ACLU can not protect the rights of those who are failing to protect the rights of others. That would be very difficult to achieve. The abortion clinic protesters are taking a side and already using violence in some instances to further their cause. The ACLU must protect those who first of all are having their rights violated.
The ACLU supports freedom of speech in all forms, however the abortion clinic protests in question are often taken beyond simple free speech or expression. Protesters often try to block access to the clinics, harass women and employees as they enter the clinic and sometimes even become violent. At that point, the protest is no longer free speech, it is a violent act that should not be protected.