The Denver Post has an article on Freemasonry which discusses the predicted Solomon Key emphasis on the Craft. Apparently Masons are worried that they might be portrayed as the 'Opus Dei' equivalent from The Da Vinci Code. According to Stephen Munsinger, chief executive officer of the Scottish Rite Masons of Colorado:

It could be very negative...we're concerned that it will say we're against traditional Christianity or established religions, or that (we're) some type of right-wing, left-wing, or off-the-wall religious sect, or that we're pushing some secret agenda for religious purposes.

Always a chance that Brown could do this, but as I've said I think it would be difficult to make Masonry out to be a bad influence in American life, when luminaries such as Ben Franklin and George Washington were 'brothers'. More likely that a sect of Masonry or a pseudo-Masonic group (Skull and Bones?) would be the bad guys, or in Brown's previous style someone pretending to be a Mason (the Jesuits?).