Consider Kim Davis. Kim Davis was a county clerk who went to jail after illegally refusing to issue a same-sex marriage certificate after the court system ruled she must. Davis, like most southerners until recently, was a registered Democrat. Until about the year 2000, virtually every southern government was majority Democratic, in some cases supermajority Democratic. The people in those parties often voted for Republican presidential candidates and were as conservative as the Republican Party, but due to inertia, they registered as Democrats. This has largely been eroded over the last 20 years. The result is that even if no one switches their opinions on anything, conservative Democrats now identify as Republicans. There are a number of inertial reasons to stick with a party that has left you behind, or to cynically join a party for a meal ticket. So, some of the apparent "era of good feelings" -- confluence between parties -- actually occurred because a big part of today's Republicans were "mistakenly" registered as Democrats. If any other region becomes one-party dominated for a long time, you'll see the reverse. The reverse is true in Hawai'i, where many erstwhile Republicans would today be simply more conservative Democrats, because the Republican party is extinct there.
There is also a belief that voters are better able to attach positions to parties. For example, if I told you that one party in the US generally favors higher taxes and higher services, and one party generally favors lower taxes and lower services, could you match the party labels to the descriptions, imperfect as they are? There is a general belief that people are better at this than they once were.
Finally, the increase in correlations between issues positions. For example, today we largely view Republicans as a rural party and Democrats as an urban party. That was not true 30 years ago. Prior to the politicization of abortion, there were constituencies that were pro-life and voted for the Democrats (Catholics being a huge such group). Now abortion is neatly aligned across party lines: there are almost no pro-choice Republicans and almost no pro-life Democrats. Ditto immigration -- which used to be cross-cutting when the union left viewed it as a threat to working conditions but now is primarily conceived along the dimension of racial conservatism. If I tell you someone loves guns, you have a pretty good chance of guessing their position on immigration, healthcare, and school prayer, even though outwardly those four issues do not need to be attached to one another.
Finally, within congress, two institutional reforms have contributed to across-party polarization: first, banning earmarks. It used to be that if I wanted corn subsidies and you did not, I would add an amendment to my bill to fund the navy base in your district. We then both vote yes. Killing earmarks may have reduced waste and corruption, but it also reduced a procedural tool used to secure inter-party agreement on contentious bills by offering concessions to the other party. It's like "suing for peace". Second, the "Hastert Rule", a rule that the Republican party adopted to never advance any bill that does not have majority Republican support. It used to be that, say, Republican leadership might advance a bill that had 40% Republican support and 80% Democratic support when those totals add up to more than 50% of the overall congress. By committing not to "roll" their own party, the Hastert rule virtually guarantees that votes that would internally divide parties and thus reveal ideological heterogeneity within the party are less likely to happen in favour of votes that divide across parties.
Why am I mentioning these trends? They contribute to a phenomenon that many political scientists (here I am thinking Tausanovitch and Warshaw, but others as well) have noted: you can perceive polarization (increasing distances between the two parties) without anyone adopting more extreme views. Rather, polarization can emerge from how party labels map to issues and how institutions surface issues to vote on. This doesn't mean no views are changing or become more extreme, but it does mean we should resist estimators that have a simplistic appeal to our gut feeling that things have become more extreme.
Some of this is discussed in the linked article, obliquely, but I think the article suffers from being written by non-political scientists trying to think about a political science problem from first principles rather than engaging with the existing literature. Reinventing the wheel can sometimes be helpful and sometimes is not.