The difference is not really in WebAssembly, but in ourselves. Back when Flash was breaking the Web, just about everyone it not just because it was insecure, unstable & violated privacy, but primarily because it was breaking the Web. Nowadays, people don't mind that JavaScript is insecure, unstable & violates privacy, and they're fine with breaking the Web.
The Web of interlinked documents is no longer an idea which captivates people: the great captivating idea of our time is the app. Nevermind that we're deploying apps atop a scripting language for a hyperlinked document system, people want apps.
Is it any different from Flash? Well, it's better-executed. It's mostly not as bad as Flash was. But it's still not great.
I don't even really necessarily mind apps. It's cool, not having to worry about Linux support from e.g. Google. But I miss the Web, and I absolutely hate when things which are static documents are turned into dynamic apps for no good reason.