Security vulnerabilities come from the same place they always have. Where IO happens, where transactions happen, and where an operating system does a lot of work. How attackers get to these points, what happens when they do, and then how the system reacts when a malicious event occurs are the factors that matter.
In today's world of complex technologies, I have yet to meet a single organization that is invulnerable to these threats. I've seen a lot of organizations limit damage, patch vulnerabilities, and generally manage their risk profile effectively - but losses are a part of the business.
IMO, the only thing that will really make a difference is when we have technologies that are sufficient enough to male the user more resilient. Only then can we have a truly safer web.