coolkid: I spent 30 years as a college counselor, and can tell you that your situation is not all that unique. What you should do is this: When submitting your college applications, I encourage you to prepare a statement that explains why your grades were so low in your freshman year. You may wish to have your guidance counselor help you to prepare the statement and also have him/her write something on your behalf.
If you are able to visit the colleges you will be applying to, make an appointment to meet with an admissions officer. Bring a copy of your high school transcript with you, and be prepared to discuss your situation with him/her. By establishing a rapport with a particular counselor, he/she may "go to bat" for you when your application is being reviewed.
Also, don't get discouraged. Of all the courses and grades on your high school transcript, the freshman year ones will be viewed as the least significant. In reviewing transcripts, colleges look at the "trend" of your academic performance over your high school years. In your case, your grades have certainly been on an upward trend. That's much better than the opposite, whereby you would have started out strong in 9th grade and gotten progressively weaker in 10th and 11th grades.
Hope this helps. Good luck!