Linux is completely free. If you, or any of your employees are familiar enough with Linux - You could go out and buy yourself a new rack mount server, or desktop/tower pc and configure and install a Linux server on it yourself, completely for free. And the only cost to you would be for the new PC. Or you could repurpose an old, or existing PC and then there is almost no cost - other than the wages of the employee who sets it up.
The expensive prices you have been quoted are for an expert to securely set up your server for you.
It sounds like some kind of managed hosting deal.
So you aren't paying for Linux per se. You're paying for someone to expertly set up Linux for you. And it sounds like they will deal with upgrading it and monitoring it.
So you're paying for the peace of mind that your server will be set up securely and managed for you.
If you, or any of your employees are savvy enough with Linux, you could save a lot of money, but your IT guy (if you have one) would have to ensure everything is configured securely, stay on top of updates, have some kind of system in place to monitor the server for any intrusions (jic) and have a good backup regime in place. Etc. Etc.
So it's all about balancing the cost. Is it cheaper to pay a 3rd party to deal with setting up and managing your server remotely? Or is it cheaper to set it up onsite yourself and have an employee deal with that side of things?
But Linux itself is 100% free! What you have been quoted for is not Linux itself, but for the service of having it set up and managed for you.