While a non-academic journal such as The Atlantic or the New Yorker pays its authors for content, academic journals get massive amounts of content volunteered to them. While non-academic journals pay an editor to hone and perfect the content, academic journals have volunteer peer reviewers and volunteer action editors doing this work for the cost of a line on the academic CV. Both types of journals offset some publication costs with advertising, but while non-academic journals sell for ~$5 per issue and under $50 for a year's subscription, an academic journal will charge $30-40 per article and thousands for a subscription. This means that the tax payer who funds this research is not able to afford to read the research.
Let's say you're an author, and you're submitting your article to a scientific journal. It gets reviewed and edited, and is accepted for publication by the action editor. Great! Your excitement gets diminished somewhat from two documents that get sent to you: one that signs over your copyright to the journal, and a publishing bill based on the number of pages and color figures in your work (often a few hundred dollars). Now, if you want to use a figure from this article again (say, for your doctoral dissertation), you must write the journal to get permission to use your own figure. Seriously. Other points against academic journals can be found in this entertainingly inflammatory piece.
But what about open access journals? Good question. These journals exist online, and anyone can read them, which is great for small libraries struggling to afford journal costs and citizens wishing to check claims at the source. They're not so great for the academic, who gets slapped with a $1000-2000 fee for publishing in them. As inexpensive as online infrastructure is these days, I would love for someone to explain to me how it costs the journal so much just to host a paper.
I was excited to read this interview with academic publishers Wiley and Elsevier on these issues. However, I find most of the responses to be non-answer run-arounds. A telling exception to this is in the first question "what is your position on Open Access databases?". Wiley responded:
"The decision to submit a manuscript for publication in a peer-review journal reflects the researcher’s desire to obtain credentialing for the work described. The publishing process, from peer review through distribution and enabling discovery, adds value, which is manifest in the final version of the article and formally validates the research and the researcher."
In other words, we do this because there is a demand for our journal as a brand. You, researcher are creating the demand. However, I do hold out hope that as more publishing moves online, more researchers and librarians realize that there are both diamonds and rough in all journals, and this will wear away at brand prestige, allowing the illusion of "publisher added value" to wear away.