Anyone could create an application. 99% of the time that anyone had 0 UX experience and created travesties that were horrible to use. So people associated the poorly designed database with the product.
From a technical point of view one of the bonuses I saw was that it used PKI throughout for encryption and such, which very little other software did. Though this was also clunky at times especially for non-technical users (has anyone ever made the use of PKI a smooth process for those who don't care to know the details?). Proper ACL management too rather than more simplistic permissions, but again this could be very clunky.
Though I'm not sure why we are talking entirely in the past tense, while Domino & Notes are not widely used anymore, they are still out there and developed (under the name HLC Notes) with the last release (adding LLM based “AI” features, of course…) was Jun last year and a bugfix update a few months later. My experience with Domino/Notes was in the 00s and early 10s when I was the accidental admin (the only guy who really understood it left) of a mail and document server based on it, hopefully the clunkiness complaints at least have been addressed since then.
Whereas many Notes applications were internal so there was no "survival of the fittest" and the UI toolkit was passable at best. As a result, many Notes users never experienced a well-designed Notes app.