I have a medical condition that could cost me my job, and I was told by my Dr to do FMLA. I'm afraid i'll loose my job if i did.

The FMLA protects you when you are out of work due to a serious health condition.  The employer is not allowed to count FMLA time against you for termination purposes.  However, if you miss work with no FMLA coverage, then the employer can lawfully terminate you in most cases.  If you are FMLA eligible and you might miss time away from work due to a serious health condition, then you should appy for FMLA.