IDK their reasons but if I were doing a thing designed purely as an in browser experience, I would lean towards three.js for most projects. Unity can compile for web, but the launch times and build sizes are pretty gnarly.
+1 for launch times & build sizes for web. Browser game bounce rates skyrocket after 5 seconds of loading, most Unity games exceed this. (I've worked on several of the large multiplayer web games.)
That said, I've met & work with _a lot_ of developers who shipped Unity for web solely because (a) they already knew Unity, (b) they could easily hire for Unity, (c) their art pipeline only worked with Unity, or (d) they aim to ship to mobile later. Built-in physics + better rendering + networking are usually just a bonus.
