Interesting article, but I only agree with it in the sense that I think that - tactically - a relaxed approach is less likely to be attacked. It's purely about stealth.
As far as why secularism is being attacked, I don't think it has as much to do with the "aggressive" nature of it's proponents as the article suggests. He talks about American being the most culturally religious but most secular constitutionally - but secularism is most certainly under attack in the States and has been for quite some time. It's fortunate that the founding fathers were so fiercely secular and so fiercely opposed to religion being entwined with the state, because it's given a foundation for freedom of and from religion. But ask most Americans and they'll tell you that America was "founded on Christianity". You have Rick Santorum going around claiming that separation of church and state is not possible and that legislation should be based on religious morals. As crazy as we know Santorum is, he's not some random lunatic, he was a US Senator, and he's considered a potential candidate for President. A significant portion of US citizens support this man. Any request to honour the country's secular foundations (such as the request that Pledge of Allegiance, taken by all American school children every day, is amended to exclude "one nation under God") is viewed as a hostile attack on Christianity.
At the end of the day, the reaction to demands for secular society is mostly shaped by the ego-centric belief held by the religious majority that their religion comes first. When you ask that state schools be secular, they don't see it as a request to honour all beliefs by not forcing children of others to undergo religious instruction, it's seen as an attempt to take religious instruction away from their children. You're violating their rights to freedom of religion by daring to ask that you not be forced to submit to them - never mind that you haven't tried to stop them attending church, from education their children themselves, from taking part in religious ceremonies in their own time. You think they shouldn't have the right to make the government responsible for their child's religious indoctrination and are therefore persecuting them.
A certain amount of it has to do with tradition, too. I think most people are instinctively conservative in that they see things as they currently are and believe that's the proper way they should be. We have a limited view of the time-scale of human history because we're not naturally equipped to think beyond our lifetime. So if religion is taught in schools, then that's just the way it's supposed to be, regardless of how "vaguely religious" you are -- anybody who tries to change that is "making a big deal". Schools in America have always been secular, so there's no argument there, but the Pledge of Allegiance has always stated that the US is "one country, under God, indivisible" so why change it? Despite the fact that it's the same underlying principle - honouring everyone's beliefs by not pressing any religion on any resident or citizen. To view it in non-religious terms, it's like the legality of alcohol versus the legality of marijuana. People assume that the latter is worse because it is currently illegal whereas alcohol has, for the most part, always been legal in Western society. It doesn't matter that they both represent the same danger when it comes to driving, or that alcohol is far more dangerous in that it is chemically addictive, wreaks havoc on a number of body organs, and is considered so commonplace that alcoholism isn't always noticed or taken seriously. But most people will fight against the legalisation of marijuana without question because it is illegal and therefore should remain illegal.
By asking for anything to be changed, you're going to meet resistance and that resistance will rarely be willing to listen to logic. In the case of secularism, there is the additional problem that religion makes people highly emotive. If anything, true cases of "aggressive secularism" have been caused because pro-secular activists have more or less been treated like animals backed into a corner. I still think that a low-key campaign focuses on the most important issues is the best option, but not because I think secular activism has brought this perception on itself.