That’s not exactly how I remember it. I recall there being both gay and gay-friendly people wondering if VW was subtly suggesting these guys were a couple. This was heavily influenced by the fact that the commercial premiered during the coming out episode of Ellen. In another context everyone probably would have figured the guys in the ad were just two college dudes wasting time, but the association with a major gay-themed media event put things in a different light – one not intended by VW, but one that the company didn’t object to either.
I was pretty confident of my memory here, but also managed to dig up a couple of cites: see the entry for the Volkswagen ad at Commercial Closet and the last section of this article.
I suspect there were probably some wacko anti-gay groups that protested ALL the companies that advertised during the coming out episode of Ellen, and the VW ad was likely the only one that featured anything resembling a same-sex couple so it would have attracted special scorn. But it definitely wasn’t only anti-gay people who thought those guys might be more than just buddies.