Interesting article. I've never been to a church that had trouble with homeschoolers. The Reformed ones especially, were full of homeschooling families. But I can definitely understand the "independent" mindset of some. I saw one church torn apart because of that issue. But I don't think it's necessarily tied to homeschooling itself. But still a thought provoking article, and something to keep in mind.
I read the first half of the article in some bewilderment, not understanding what the issue was since he didn't seem to have churches that are actively hostile to homeschoolers in view.
Then I got to the part where the author seemed to be against ANY and ALL age segregated activity, not just during the worship service. Being totally against any kind of age segregated Sunday School (even for the smallest children) or without exception against any kind of youth group is an extremist position, in my opinion (although I do not think such activities are indispensable, either). The homeschool families I know are not like this at all. If I'm not misreading him and this is his position, then no wonder he has had trouble. This position isn't too far from those who usurp the authority of the eldership and have the head of household serve communion to the members of his family.
Much of the rest of the article was good, encouraging independent minded folks to either join the best church they can or start new churches instead of being defeatist and abandoning church altogether.
I think some of the reason for suspicion is this: Some people would rather preach homeschooling (or fill in the blank with the name of some other movement or activity) than Christ, making that their whole raison d etre, and viewing even those who prefer Christian schools to be apostate.
He was honest on his position...you read him right. But if you read the rest of the article, you will find that he also did not encourage "ursurping authority". That is part of the point...that simply following ones convictions in an area such as age segregation is often viewed in and of itself as an ursurption of authority.
I believe he was honest in that there are assumptions on one side and that there are precautions that should be taken to keep from adding to those assumptions. And yes, that we shouldn't simply give up on the church altogether.