First of, it was very ahead of it's time in it's depiction of the internet. Mainly because Japan was also ahead of the west when it came to stuff like imageboards. For most people, lain isnt as much about the rather cryptic story as it is about the overall aesthetic of the show.
There many recognizable unique scenes and sounds, like the humming of the electricity lines, the sounds-scapes they used to represent the flux of data...
It's very relatable, especially to people who grew up with the early internet.
Lain isn't about sex appeal, it's about the mysticism of a new area, the explosion of the internet as a vast, unexplored space. Many anime from the time period play with similar ideas, most notably of course, Ghost in the Shell.
Tl;DR yes you have to have a certain mindset to enjoy the show, maybe borderline autistic. It's an age thing, I suppose. I remember when the internet was still vastly different.
One time I was browsing a fairly professional/mainstream website and suddenly all this guro shit popped up. Like girls cut in half with chainsaws and shit. That would never happen today. That kind of internet is dead, and lain serves as a reminder of that time period.