There's no disputing that the feds are going after a lot of state and local officeholders these days. Since 2002, both the number of public corruption cases and the number of FBI agents devoted to such cases has increased by more than 50 percent.
Many of the investigations and prosecutions have been warranted. The question is whether they've been targeted at state and local officials who happen to be Democrats.
Given the vast discretion prosecutors maintain in picking their targets, they are subject to regular complaints that they are interfering with the political process and the normal operations of government.
Since corruption cases tend to be headline-grabbing, there's also reason to be concerned that U.S. Attorneys will pursue weak cases for their publicity value.
That sort of motivation was starkly on display in 2004, when e-mails leaked from the office of Thomas DiBiagio, then the U.S. attorney in Maryland. He demanded that his staff bring no fewer than three "front-page" corruption indictments by Election Day.
The linked article notes that federal prosecutors are better positioned than state and local prosecutors to pursue state and local political corruption. The article also notes that corruption is easy to find, although federal statutes authorizing prosecution for the theft of "honest services" are so vague that it's difficult to tell when a politician doing business as usual (appointing a campaign contributor to an oversight board, for instance) is violating the law. And the article notes that successful prosecution of actual corruption can persuade state and local governments to do a better job of policing ethics and cleaning up the political process.
All of that is true. In addition, it's better for the feds to pursue legitimate corruption cases that can cause enormous harm to public treasuries than it is to chase drug dealers. When the federal government indulges in questionable prosecutions like Siegelman's, however, and when federal prosecutors seem more inclined to go after Democrats than Republicans, the fear that prosecutors are out of control is reasonable.
Given the amount of corruption in the Bush administration, the FBI ought to be paying just as much or more attention to the national government. State and local corruption is comparatively small cheese compared to what's happened in Bushworld.