The governments pay a researcher for his production. One way to measure how productive is a researcher is by how many publications does he has during the evaluation period. Other stuff is included, of course: lectures, graduated grad students, the citations of your work, conferences, invited talks, and how hard is to get a publication in the journals you are publishing... well, the variables depend on the country, but that's the idea.
The nice publishers joined forces to facilitate this evaluation, with the hope to make them easy to follow up or to evaluate a researcher. They created a web site, the web of science, where the authors can check the publications, references and citations of their work of from other researchers, in an automated way. When you are applying for funding, you just give the ISSN number of every publication you had in the evaluation period, and that's it, you print it, or send this information to the government, they get your publication record, citations, etc., etc., and renew a contract, get a promotion, or give you thanks.
The problem is... you need to publish in a journal from the circle of publishers who maintain this website, if you publish in a journal not from those publishers, then, your publication cannot be counted by... by the government, hence, you won't get a payment rise, or your contract will not be renewed. Since the government only checks this website, then everybody must publish on the publishers in that circle. And that's where the bad thing comes: offer/demand, you only publish with them, then, only those publishers have the good journals, if those are the journals where everybody publish, then, the good research is in there, hence, they can ask for more money to read their top journals. You need them to do research, and your research will be published there, so you can have a job.
That's it, it is just a circle that went wrong, but now everybody is mad at the publishers. The problem is that the governments are helping a bit on this.
Alternatives to this web of science, are very few: Microsoft Academic Search, Google Scholar, (Academia.edu, Research Gate?), but none of them as "professional" as the web of science in the eyes of the governments, so you just continue using the Web of Science.