I got an F in a 1 unit lab course because I thought I dropped it, but I didn't. Took it again and got a D. Took a 3rd time got an A lol. I also have an F in a 3 unit course which I repeated as well and obtained an A. I know AMCAS counts both, so with all courses taken considered my GPA is 3.59. Obviously my situation is going to require some serious explanation during interviews, but the rest of my application is strong and I have shown proficiency in much more difficult upper division courses of the same subject matter.
So basically I'm going to give the usual advice: demonstrate a strong upward trend, be prepared to explain this in your interview, raise your overall GPA, demonstrate proficiency with A's in upper division courses (if the course relates to your major or pre-reqs)
None of my poor grades were in a pre-req course. Obviously one should consider a D in a pre-req more damaging than in another course. I definitely suggest retaking it. Especially if you plan to apply DO because in that case your original D won't be considered and that might help your GPA out a bit.