Whether you are a 1099 subcontractor or an employee is really up to you and your principal/employer. While what the principal/employer does as far as controlling how you perform your work, etc. goes to whether they are liable for your actions or not, whether you are a 1099 subcontractor or an employee is a discussion to be had and a decision to be made between you and your principal/employer. If you don't like your status as a subcontractor, then your primary option really is to quit.
This answer does not constitute legal advice as all the relevant facts have not been provided. Additionally, no attorney-client relationship is created or exists between the questioning party and the answering attorney. We recommend that you consult with and possibly retain an attorney to discuss and evaluate all of your rights.