Advertising is only one reason. There are still conflicts of interest. And the journals still have to abide by their Allopathic medical paradigm, which supports vaccines. Readers would think they are crazy if they started publishing anti-vaccines articles. So the journals are stuck with supporting only that one medical model.
I said I don't trust peer-reviewed studies from scientific medical journals. Not trusting them doesn't mean that I'm against each and every one of them. My point is that they are commonly not as truthful and not as unbiased as most people believe them to be. I'm always open to reading new things, such as these peer reviewed studies, but when there are sources like Tenpenny and Miller who say that vaccines can cause diabetes vs. journals who say vaccines don't cause diabetes, you have to pick the sources that you think are reliable. Peer-reviewed doesn't necessarily make something more reliable.
Is there limited transparency in medical research? Yes. Often. It's something that needs reform. There needs to be more independent research performed on the benefits AND RISKS of vaccines, because there's bias on both sides of the debate (I'm looking at you, Andrew Wakefield!) Is there a problem with the peer-review process? Yes. However, peer-review is essential to good science - something that you don't seem to grasp. In short, does peer-review make an article more reliable? Absolutely. You need a blind review to scrutinize your work, to make sure that you've included all the relevant background material, controlled for the confounds to the best of your ability (and discussed those you can't control for), and analyzed your results properly. These reviewers don't get paid for this. They are not revealed to the author. They are not tied to the studies. They don't directly benefit from it's publication, and since there are several reviewers for one study, they certainly don't have full say in the outcome.
You're talking about reliability as an emotive trust that you hold for the researchers based on the values they hold in general. That is not science. It's a perfectly reasonable argument for why YOU feel more comfortable with their advice, but it doesn't speak to their credentials or validity at all. Science is an important part of the debate, whether you trust it or not, and peer-review is probably one of the most important processes in scientific research.
I'm starting to feel like my head is banging on the wall here, so I'm bowing out. Again, having reasons you trust your sources over others is your perogative. However, it's (almost too) easy to call your sources' credibility into question as well, so their science (including blind peer-review) is what gives them any strength of conviction.