If you as a company give/sell Linux to another company/consumer, you have to warrant for it. If Linux is violating IP-Rights (possible risk: SCO vs. the World) you have to indemnify you partner when he cannot use Linux any more or has to pay for it. Can you imagine how much money that is when you have supplied a large consumer like a bank with Linux and their whole production is on a standstill for one or two days?
You have to provide patches for problems with Linux ASAP, i.e. you cannot wait until the community has fixed the problem. You even cannot wait if the community is working on the problem because if not you have lost several days and you partner could hold you responsible for any damage resulting from it. So you have to have some Linux programmers to fix the problems on standby. If, on the other hand, you buy the software yourself from a partner such as Microsoft and a problem with their software arises you will give the OS seller hell to fix it for your customer. And yes, even Microsoft bows to this.
Oh, another problem with open source software for a company is of course the GNU/GPL. First you have to make your work on the product open source itself which means you have to provide your work the customer paid for to gain a business advantage to his market opponents as well (your customer is not delighted about that) and you cannot impose most of the warrant limitations in the GPL to your customers because they violate national law. Oh, if you use Linux in a confidential government environment you are in for another problem: Try to preserve your NDA and to make your confidential government work open source at the same time.
