From Daniel Dreisbach: http://www.christianitytoday.com/history/2008/november/misusing-history.html?share=9iiOSaVXTxMjHIO3NzG3DaO6fW8WI0w8
First, Jefferson's metaphor emphasizes separation between church and state—unlike the First Amendment, which speaks in terms of the non-establishment and free exercise of religion. Jefferson's Baptist correspondents, who agitated for disestablishment (the elimination of an official "state church") but not for separation, were apparently discomfited by the figurative phrase. They, like many Americans, feared that the erection of a wall would separate religious influences from public life and policy. Few evangelical dissenters challenged the widespread assumption of the age that a self-governing people must be a moral people and that morals can be nurtured only by the Christian religion. They believed religion was an indispensable support for civic virtue and political prosperity, and its separation from public life necessarily imperiled social order and stability.
Second, a wall is a bilateral barrier that inhibits the activities of both the civil government and religion—unlike the First Amendment, which imposes restrictions on civil government only. Replacing the First Amendment with a wall unavoidably restrains religion, especially in its ability to influence public life, thereby exceeding the limitations imposed by the Constitution.
Third, having assumed the separation of church and state, the civil state (often acting through the judiciary) has then presumed to define what is "religion" and what are the appropriate realms, duties, and functions of the "church" in a civil society. This has given the civil state practical, de facto priority over the church, subjecting the latter to the jurisdiction of the former.
Those who criticize modern constructions of the wall are not necessarily supporting a religious establishment. Rather, these critics contend that the First Amendment requires that religion and religious perspectives must be allowed to compete in the public sphere, without government inhibition, on the same terms as their secular counterparts. By its very nature, however, a high wall does not permit this.
The use of Jefferson's metaphoric wall to exclude religion from public life is at war with our cultural traditions insofar as it shows a callous indifference toward religion. It also offends basic notions of freedom of religious exercise, expression, and association in a pluralistic society. Unfortunately, the Supreme Court's "high and impregnable" wall has redefined First Amendment principles, transforming a bulwark of religious liberty into an instrument of intolerance and censorship.