In a perfect world, every software we are using to communicate via network would always communicate using strong encryption. We would also have access to 100% trustworthy and reliable keyservers and certifacate authorities. But unfortunately we aren't living in a perfect world.
In the real world, we have to deal with lots of software which doesn't support encryption, doesn't support sufficiently strong encryption, doesn't support encryption in a sufficiently user-friendly or practicable way, or has faults which cause it to inadvertedly communicate unencrypted.
A VPN software usually provides a virtual network interface which, from the perspective of software, works like any other network interface. Applications can use it without being aware that it encrypts their communication. That means they no longer need to implement encryption on their own because the VPN software takes care of it automatically.
But keep in mind that this only applies to communication which doesn't leave the VPN. When you use a proxy server on the VPN to communicate with the public internet, you have to make sure that either the proxy encrypts properly, or that your software does.