a. I admire your courage, if not your intelligence.
Does that mean
b. I admire your courage, but not your intelligence.
c. I admire your courage, although I am not sure whether I admire your intelligence.
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Your interpretation 'b' is correct. The form "A, if not B" is usually a rhetorical device where the 'if' is intended to be taken as false. Paul and Kate's comments do a good job articulating the sentiment that might be behind this statement, with the intended meaning that even though the speaker doesn't respect your intelligence (or the intelligence of your decision making in this case), they do respect your courage.
Some other examples of this usage are 'Your research was interesting if not very useful' and 'At our board meeting James was present, if not engaged.'
Keep in mind that this is not the only use of "A, if not B." The other common use is for two different degrees of a similar condition, where it's unknown if condition A or the more serious condition B is actually the case. Examples of this form are 'If we can't obtain a codebook, breaking the enemy cypher will be difficult if not impossible' or 'With the way you've been treating it, that rope is likely frayed, if not snapped entirely.'
There's no perfect way to determine which usage is intended, but a pretty good guide will come from applying these two principles: