Tolerating another's beliefs does not mean sharing them; it simply means not disrespecting someone only because of their beliefs. Some beliefs, however, should be discouraged in a free society.
How can a society be free if it discourages some beliefs? Shouldn't all beliefs be respected equally? The answer is "no." Beliefs that are antithetical to freedom and mutual respect - important traits of a free society, IMO - should not be tolerated, and it does not offend traditional notions of freedom to be intolerant of such beliefs.
For example, American-Muslims' belief in the five pillars of Islam should be tolerated by all Americans, even if most Americans do not share such belief. However, Americans should not be required to accommodate a "belief" that America should be transformed into an Islamist state against the will of non-believers.
Similarly, Christians’ belief that Jesus is our lord should be tolerated by all Americans, even those – including myself – who do not share that belief. But, Americans should not feel compelled to accommodate a “belief” it is okay to cajole, harass, or otherwise emotionally blackmail non-believers into going to church. Nor should Americans tolerate a belief that it is proper to teach children that doing such is okay.