To me, Lain was designed so you could interpret it the way you want to.
Personally, it's a story of our human identities merging with the personas we establish online, seeing that communications and connection become more ubiquitous all the time.
In the same way, how our collective history is always changing, adapting to fit in our new experiences, and reinforcing the best memories. In that way, our reality becomes a construct, a shell we extrude from our personal experiences and what we gather from the rest of the society.
Or you can see it as more of a Digital GAIA scenerio of singularity, where the global network grows so complex that intelligent patterns start to emerge. The planet as a whole being an emergent system. Lain serves to represent this new kind of digital god.
I could be wrong. But, fuck yeah, transhumanism!