Your experience definitely doesn't match mine. That said, I was not doing the same sort of work as you, so I will mostly limit my complaints about Notes to general usability. If someone is getting specific functionality out of Notes they couldn't get anywhere else, I can see somebody overlooking all of this.
I don't remember what year I started using Lotus Notes, it was at least 1995, I was using it on Windows 95 and on Windows 3.11. I was working summers during college. What's incredible about Lotus Notes is how we're now in 2012 and it still has some of the same bugs, same UI weirdness, and it's still pretty much just as slow.
I think it's hated for pretty straightforward reasons, things like how it doesn't conform to your operating system's usability guidelines, it still more or less acts like the mainframe application it was derived from; so when you'd press F5 to refresh it would instead close the window (if you want to refresh, you have to press the square in the corner, where you know there's an invisible widget that refreshes--you just know because you've used it for so long.) There's that weird tile screen where you click a tile and it indents like a button being pressed, but then just stays there and does nothing--why??? It's slow no matter how fast your computer is. It crashes. For years when it crashed you had to completely restart your computer of Lotus refused to run (who remembers when KillNotes was invented so you didn't have to do this???) It does things in just plain weird ways that cause weird side-effects, like how selecting multiple documents to delete would clear your clipboard. Bugs that seem unacceptable for an enterprise project, like when I would reply to someone and it would send the reply back to me instead of the sender. Or how selecting documents to archive and archiving them only archives about 85 percent of them, so you get in the habit of selecting the same batch to archive, over and over, as it progressively successfully archives only a portion of the documents you selected, until they are finally all archived. These are only a few complaints, there are many more.
I used Lotus Notes at every job between then almost all the way up until now. Some things got a little better; they fixed a bunch of the bugs, when it (only occasionally now) crashes you don't have to restart your computer. F5 doesn't close your window. You almost never see that near-useless tile screen. And there are the things that Lotus Notes has always done right, like how it's had built in signing and encryption since forever. And the document store, as is the original point of the article, was pretty cool at the time, but IMO you really needed an Notes expert to keep it all together for your business, where document stores now are pretty easy.
Sorry if this was long and negative. But every time there is discussion about Lotus Notes I feel compelled to talk about my long term experiences as a user (as opposed to admin, or content creator) of it. I think there is definitely a reason it is hated.