10gen was a startup and MongoDB was built to make money.
You can keep a project "open source" while offering enterprise level of support. Look at Puppet, Chef and now Ansible.
The world needs business. Nginx is mature and actually deserve to run as a business. The developers are already consultant for a long time; they just want to monetize Nginx publicly, as a startup.
Are you afraid Nginx will become the next Microsoft Windows Server? I can't predict future but with 100% of faith I say nginx will be fine in the next several years.
I don't necessarily think free software == win.