I think you've misunderstood what's happening here. Zerodium, the company mentioned in this article, is an exploit broker. They buy vulnerabilities from researchers, then sell them on to government intelligence agencies. The entire purpose of their business is to undermine the security of the tools we use.
Bug bounties are a response to this trade in exploits. They incentivise researchers to publish vulnerabilities rather than selling them to spies. They're a necessary evil to keep zero-day vulnerabilities out of the hands of oppressive regimes. It's not nice, but that's just the world we live in.
Large companies that rely on open source software have started to understand the importance of financially supporting OSS development, largely as a result of the Heartbleed crisis. The Linux Foundation's Core Infrastructure Initiative has created a secure financial foundation for critical open source projects.