The ultimate source of the conflict between the Federal Government and the States is that there really is no clearly defined line in the Constitution where the Federal Government begins and where the States end.
There has always been overlap, hence, there has always been friction.
With regards to the first part of your argument, which I read with some amusement. (I was listening to the same report, haha. NPR is quite popular in this "Haven of liberals and criminals" Massachusetts. (to quote Bill O'Reilly) The political parties have never really held to any kind of agenda or ideology or platform, they just instinctively attack whatever the other party is doing. That's American politics.
Take, for example, the current spate of criminal indictments against high-ranking Republicans? Some have asked, "Why now, all of a sudden?" The answer is simple: it's retribution. For decades, the Democrats and the Republicans maintained an unspoken agreement to keep stories of one another's corruption out of the public eye as much as possible in exchange for the same from the other. This is, of course, why Kennedy's numerous extra-marital affairs were largely ignored.
In the 90's however, Newt Gingrich's "New Republican Revolution" ensured that a lot of new, young Republican lawmakers with more ideology than brains were elected. They were the ones to have President Clinton impeached, sullying what would have otherwise been a relatively clean and prestigious historical record.
The Democrats, of course, saw this an act of aggression and immediately began sanitizing themselves for the upcoming political assault on the Republicans. Which, of course leads us to the present day, with major indictments and allegations against practically every major Republican leader.
