Do I have to pay for workers comp in GA?

I don't practice WC in your state but I have practiced WC in Virginia for 35 years. The fact that your employer is giving you a 1099 and not a W-2 means he is regarding you as a subcontractor. You can choose not to work for him. There are a number of occupations such as painting for example where there is a fine line between the worker being either an employee or a subcontractor. If you are a skilled worker, you may want to look elsewhere and work for an employer who will treat you as an employee and not a subcontractor.

Lisa is correct. He is withholding WC insurance on you as if you are an independent contractor. Many small companies try to avoid the cost of workers comp insurance in this way, especially in this environment. If he has 3 or more employees, not counting any officers or directors, he must carry the insurance. He could argue that he is not an employer, just a general contractor. There are many specific facts and circumstances that must be present for you to be an independent contractor instead of an employee. But you do not have much of a choice here. You can take the job with the deduction in pay or turn it down.