Free speech, whether articulated or symbolic, does not have to be *popular* speech. This is an important distinction to make when discussing the First Amendment's passages on "free speech". The unspoken words at the end of those sentences is "by the government". The Supreme Court tends to view provocative acts such as flag burning with an eye towards *governmental* response, not necessarily a social response.
Can a government representative extinguish a burning flag held by a protestor? No, not legally. He or she has every right to be offended, and to denounce the act in a public speech or press release after the fact, but the burning of a piece of cloth which represents a US flag can only be interpreted as symbolic speech.
I believe the case involving the Boy Scouts came down to the rights of private organizations. The protections offered by the First Amendment only extend to governmental agencies, and the Boy Scouts are not part of the government. An individual who was denied membership because of his race or sexual orientation or other consideration can still pursue a civil suit, but the organization itself is not legally required to follow the same rules as government agencies.
Parents can choose not to allow their children to participate in an organization they feel is exclusionary or prejudiced, but the federal government cannot force the Boy Scouts to modify their internal criteria for membership.