It still depends. There are a lot of factors. And quite frankly how the product is licensed is way down on the bottom of conserned. Most organizations are able to negotiate better contract with these companies. Do you think a 1,000+ employee companies will be using standard windows licenses? No they will negotiate with Microsoft for a license and conditions that fit there needs. With FOS it is what you get that comes with it. If it is GNU you better be sure that you don't use it in your product if you want to sell it. BSD, MIT and Apache licenses also have their own issues but you get what you get and often have little chance to negotiate with someone to make it suit your needs.
There are costs to an organization that isn't to the individual. For the individual the time wasted learning a FOS software is their own time and often enjoyable hobby. But to a company have to pay someone to learn this is expensive and there are factors such as product lifespan, and ability to find employees who knows how to use that tool and training resources available. All these factors makes the license cost a drop in the bucket.
Not FOS is overall a good thing and companies shouldn't shy away from it there are a lot of professional tools out there that can save you a ton of money. However not all of them.