What Gallup is talking about here is the margin between the two parties, how far apart the approval ratings are. Using the first available Gallup data from each quarter of every presidential administration since Eisenhower, the margin between the two parties looks like this.
You can see that 9/11 made a big difference in the first year of the George W. Bush administration. The partisan split plummeted in the wake of the attack, but then quickly rose again as the conflicts in Iraq ad Afghanistan became unpopular. (The two presidents that saw a very small partisan difference at the outsets of their terms were Ford and Johnson, for reasons mentioned at the top.)
Running just under Obama and Bush are presidents Reagan and Clinton. If you look at opinion by party during the second term of those two presidents, they're similar, with some fluctuations in the middle of each line.
If you compare Obama's and Bush's second terms, though, the similarities are remarkable.
Look at the continuous distance between the lines.
Jones offers some explanations in his analysis. "These increasingly partisan views of presidents," he writes, "may have as much to do with the environment in which these presidents have governed as with their policies, given 24-hour news coverage of what they do and increasingly partisan news and opinion sources on television, in print and online."
In other words: The environment that has polarized politics at large has, as you'd expect, polarized the presidency as well. It takes a tragedy to overcome that, it seems. So perhaps, in one sense, it's for the best.