Praying in Jesus' Name

Consider this:
The Committees of Correspondence in Boston, 1774, penned a rallying cry for independence that was later used during the Revolutionary War:
"No King but King Jesus!"

Now the same country that started that way is hearing court cases about prohibiting city council members from ending the opening prayer with "...in Jesus' Name." In the example linked below, one of the members of the council is a minister. The members do the opening prayer on a rotation basis. Naturally, the minister wishes to end his prayer in the way most comfortable to him, but this has offended at least one person present at the meeting. The ACLU threatened to take the city to court about this.

It seems odd that the same ACLU will stand up for free speech, even when the speech is very offensive to Christians. So why isn't this minister's prayer protected as free speech?

Court challenged to allow Christians right to pray, too