I used Lotus Notes for many years, starting with version 3, and I got the impression that there was some sort of philosophy behind it, but I just couldn't figure out what it was; I admit I got tangled up in the interface. A good friend of mine was a Lotus Notes admin, and while I believe he "got it", the hoops the interface made him go through to do various tasks (backing up a database by copy-n-paste because it was the only "reliable" way?) negated whatever deeper benefits the platform provided.
Ultimately it comes down to execution; the web has its shortcomings, but it's simple enough that people "get it" and can use it effectively. Being relatively simple and text-based, it encourages experimentation without needing to worry that the underlying database can somehow can be corrupted or external links permanently invalidated. It doesn't hurt either the the web itself is basically "free", while Notes was (is still?) quite expensive.
I don't want to get all Godwin here, but I think a decent analogy is that Notes is a Tiger tank; sophisticated and extremely powerful, but ultimately done in by the cheap and plentiful Sherman. It doesn't mean that the Tiger wasn't better than the Sherman, it's just that the Sherman won by sheer volume.
Ozzie may be a brilliant guy, with an IQ of 100!, but if he can't execute his ideas in a way that people nowhere near as smart (say, 2!) as him can use, what's the point? History is littered with people who had brilliant ideas but are forgotten because they botched the execution. Having used both Notes and Groove (as I understand it the only other actual piece of software Ozzie actually worked on), he took a serious leap forward, just down the wrong evolutionary path.