Medicine is an independent and solitary career in many ways, and from your initiation in medical school, you're taught to make your own decisions and to develop an independent mindset. That was an ideal perspective when medical practice was driven by independent practitioners, responsible for every facet of practice and office. However, today that represents somewhat of a mixed message that can be confusing at best and downright infuriating at worst.
Here's the problem. At the practice level you're probably about 80 percent in charge. That is, while most organizations stipulate by contract or other means your independence in medical decision-making, they are in control when it comes to formulary, ordering tests, making referrals, records management and other issues. So, get used to intrusions into your exam room.
Outside the patient interaction it's their ballgame. The staff, your benefits, working conditions, etc.... it's all theirs. But, before you start grumbling, know what that means.
First, do you have a contract? If you do, then the rules are spelled out quite specifically - if not always quite clearly. So speak with an attorney. Don't play lawyer. Find out exactly what each clause means, what it limits you too and what obligations you and the organization have. Hopefully, you have done this before taking the job, but if not certainly do so as soon as possible afterward. Also, clearly understand the termination clauses, noncompetes, etc... and use examples when discussing for added clarity.
If you don't have a contract, then you're likely an at-will W-2 employee. In that case you have all the legal protections your state offers every employee in your classification. Again, speak with an attorney and talk about "what if's" in the work place to get a clear understanding of benefits as well as limitations. And, bring along your benefits and policy books for the attorney to use a further, and very important, reference.
The bottom line is this. Know your rights, your responsibilities, your obligations and your employer's obligations. Medicine teaches you to perform as a knowledge expert, but employment, successful employment, requires a different mindset.
If you're not familiar with the term "Knowledge Expert" or "Knowledge Specialist," you may find it helpful to understand the designation better and to learn how to help yourself better fit into an organization. Definitionally, most physicians are Knowledge Experts/Specialists. This is a book I regularly recommend to my clients. "Thinking for a living" by: Thomas H. Davenport.