As someone who was homeschooled, I've paid a lot of attention to other homeschoolers on this point, and I've noticed no abnormal tendencies in social skills that one couldn't just contribute to normal environment changes. It's just a baseless BS stereotype, first off, most homeschoolers are not at home for religious reasons, my sister and I certainly weren't, the only church we ever attended growing up - and that rather infrequently - was a Unitarian Universalist church and the only anti-social habit instilled in me from that was I started drinking coffee at 4 (big pack of yuppies) and have been a regular coffee drinker from age 7.

Most homeschoolers have programs they use, and socialize their kids with various social groups, even the ones who do it for religious reasons.

What you have, and it is rather clear, is a standard exposure distortion. You likely only notice someone is homeschooled when they are awkward. Many do have initial problems first entering college, rarely much different then anyone else though, it's like changing schools or jobs, and they are forewarned of this. It's practically like a secret club, I've known lots of homeschoolers and we tend not to mention it. None of them stuck out like sore thumbs, some of those from genuinely serious religious backgrounds do, typically only initially, but often would anyway. I've never met a homeschooler, with a few exceptions of some who just emerged into normal environs, who was even vaguely distinguishable from the wide spectrum of behaviors that emerges from normal pub-ed schooling. Most likely, you have met the exceptions to the rule, and never known that you met lots of homeschoolers and just didn't know it.