I watched the first episode and… To answer this
I’m going to say yeah, this reaction is not unusual. What’s weird is that my reaction was like Author’s. I think when I was a kid I didn’t have that kind of experience–to be honest it’s hard to see who did, at least on some sliding scale, because it’s not a binary determination. We homely and quiet nerds are often put into situations like this, and different people have experienced/suffered varying extents. What we see in Watamote is albeit an exaggerated version of something, but at the same time it’s easy to see how real people can have had it worse than Tomoko.
It “hits home” for some people, that is why they like Watamote. It “hits too close to home” for others, that’s why they think it’s humiliating.
But don’t you feel humiliated when you watch, say, Love Hina? I definitely felt that way about the nth time Keitaro walks into a half-naked girl, and I don’t really have any connection with K-taro in the way that Watamote is building things up. The odd thing is, the Watamote anime reminds me vaguely of B Gata H Kei, which is actually a story premised on the core idea of embarrassment (and I definitely don’t relate to Yamada). Watamote, so far, is more about self identity and pride. Well, that’s kind of related. But the tone of the two shows can’t be more different. Probably because one show is actually funny? In the riotous, raunchy teenage sit-com kind of way?

The irony, though, is that Watamote is the story of someone who struggles to connect with people because this “society” reacts to that sort of a narrative with embarrassment and shame. I didn’t really hear anyone get angry or passionate about Watamote, other than those who “hit home.” For those people God bless your souls and what not. For the “hit too close to home” people, please realize you are what Watamote is actually about–either as part of the problem (eg., society) or as a victim who just hasn’t quite gotten over it. I’m inclined to think all of us are one of the two types of people at some point.
Personally, I think this is all the by-product of self-depreciating humor for a crowd that don’t enjoy hurtful and self-depreciating humor. Basically, can you 8man? And it’s true–it certainly doesn’t have to be enjoyable and it isn’t for a lot of people. But the same goes for everyone else who can (including the people who created Watamote, who have the same problems, and wrote about them in such an open way) enjoy the humor in Watamote, the slow burn, the helpless flailing of arms. There’s a sense of helpless at play here, and you know how that goes.
TL;DR – One man’s joke is an insult to another man’s mom.