The main reason for an article being rejected is probably that it has been sent to the wrong journal. You have to think of the target audience i.e. the readers of the journal. It needs to fit the article’s subject and form. If you are a young scientist it may be difficult to assess the full range of different journals so you should seek advice from experienced colleagues or your mentor when choosing a journal for your paper.
On PubMed’s website you can search in the various journal names. Go to www.pubmed.com and then on the front page you see a link to the “journals in the NCBI-database”. This is a search engine, where you can search the titles for different journals and it can be good inspiration when selecting a journal for your article. When you have found a possible journal, then go to the journal’s website and examine its purpose and instructions for authors. It is a good idea to walk through the last couple of volumes of the journal to get a sense of whether the journal will be a good fit for your paper.
Price may certainly be an issue and only the non-open access journals are free of charge. So check carefully how much it will cost for that specific journal before submitting the paper. In most research groups it is also of importance to strive for a journal with an impact factor as high as possible. You can look up the impact factors in the Journal’s Citation Reports database on the internet.