Unbeknownst to most Southern Baptists, the money they give each week is being used (in part) to fund an organization known as the Ethics and Religious Liberty Commission. The ERLC serves as the public policy arm of the SBC. The ERLC is, essentially, a lobbying organization. They attempt to influence government officials on behalf of the Southern Baptists whom they purport to represent.
The problem is that we Southern Baptists are a varied bunch, and, while we may largely agree on certain public policy issues (e. g. restrictions on abortion), there is also much disagreement. Political positions are, to a certain extent, underdetermined by Scripture. We can agree, for example, that based on a biblical understanding of our duties toward God and man, that we ought to provide assistance to the poor and other disadvantaged members of society, but we might disagree strongly on which policies will best help us achieve that goal.
Consequently, while Southern Baptists are united around certain theological convictions, our political views may differ widely. For example, my pastor and I agree on virtually every theological issue of any importance. However, I imagine that if we were to have a frank discussion about politics we would find some significant areas of disagreement. That shouldn't be a problem. As Southern Baptists, we're united for the sake of the gospel, not politics. Certainly I believe that my political views are more consistent with Christian ethics than other views or else I wouldn't hold them in the first place. I'm sure other Southern Baptists of different political persuasions feel the same way, and it is our right (perhaps even our Christian duty) to try to persuade one another.
In and of itself, our divergent views are not the problem. The problem is that we are all, whether we know it or not, funding an organization that is advocating a very particular political viewpoint, a political viewpoint that many (probably most) Southern Baptists do not share.