Advocates of open source emphasise that, because the source code is freely available, everyone can extend or debug open source software to meet their needs. The reality of things is that few potential users of any type of software have the knowledge, the time or the desire to delve into the code of the software they are using to debug or extend it. Most people want their software to work out of the box and have someone to turn to when it doesn't. A traditional software company that sells a license will sell a support contract with it so you know what to do when things go wrong. The support provided might not always be as good as you'd expect but at least the mechanism exists. With open source software, you don't have this possibility. When things go wrong, you have to turn to newsgroups, FAQs and other sources that are usually written by developers for other techies. If you are not a techie or lack knowledge in the particular field of the software you are using, it can be very difficult and frustrating.
Another aspect where proprietary software can be more cost effective than open source software is training. Companies that produce and sell complex software will also sell training courses to enable their customers to make the most out of it. When I was working for Reuters, ages ago, I went on courses at Sun and Sybase. Those courses probably saved us a lot of money in the long run because they enabled us to understand the products of those companies better and to make better use of them. Also, through the interaction with the trainer and the other students, we were often able to relate the courses to real life scenarios that we had faced. With open source, you are usually limited to online resources or books such as the excellent O'Reilly offering. The problem with this approach is that such didactic material usually answers only part of your problem. You can't just ask a real person "how would I solve this particular real-life situation?"
The solution to both problems with open source software is to have a support contract with a company like Red Hat and this is what makes the cost of open source.