I wish they told you more about the methodology. From what I can see, it looks pretty sloppy. The lists appear to go from top to bottom according to the bolded number, except Damages, which looks like it should be tied for 14. It also looks like The Good Wife should be tied for 6th on the Republican list, kicking off 2 and a Half Men. It is clear they aren't looking at the difference between the R and D numbers, since the order would be totally different in that case. So it seems they just cut it out of the R list to make it so they were totally different. Like I said, sloppy.
It would also be nice if they gave a margin of error. These things are typically pretty hard to sample, so it is probably pretty big. If you assume a margin of error of 20 points (a real one would be a percentage, but that's more work), then all but three shows disappear from the R list except three (Beck, Amazing Race, and V). Meanwhile, only two shows (Good Wife, Friday Night Lights) disappear from the D list, and the differences are bigger overall.
If I were to guess, I would say that, except for the explicitly political shows, this isn't caused by a difference in politics, but by cultural patterns that affect both political identification and viewing habits. It looks like these R cultural patters cause them to avoid shows differently from the national average, while D patterns cause them to seek out shows. Given that the D shows don't look to have especially high ratings, it looks like the R avoidance is the dominant cause of the difference. But you'd need real data to say anything with any surety.