I received a 1099 from my employer for whom I drove truck for last year. It said I was paid just under 12,000. I also received a w2 and my wages were under 2,000 and showed deductions. The only pay stubs I received from that employer were with the last 3 checks I received from that employer. The 3 pay stubs reflected the info on the w2. Before that I was just getting a check and didn't worry about pay stubs because it is a small company and I figured they didn't have the proper computer payroll software to print me a pay stub but then after about 6 months they were able to print paystubs. I don't understand what the 1099 is all about. Did this employer not take out the proper deductions from my pay? Isn't it an employers responsibility to take out deductions, and pay unemployment and labor and industries insurances? I suspect this employer has pocketed the deductions, did not pay insurances and at year end is treating me like I was a sub-contractor by sending me this 1099. This has really hosed me trying to do my taxes. How can employers get away with doing this kind of thing? What can I do about this? I do not have a contractors license or business to where I can have enough deductions to alleviate paying so much in to the IRS.
What can I do about this?

The first question is what salary were you hired out and did the checks you received (before the last 3) reflect that salary. If they did, then nothing was withheld and they were paying you as a contractor.

What it sounds like to me is that you were hired as a independent contractor (not atypical for truckers), but, for some reason, they changed you to a salaried position at the end of the year.

If your checks were less than the full amount they agreed to pay, then you will have to prove it and go back to them and ask what happened to the rest.