The black borders are created by the Adobe Media Encoder during encoding to FLV, to handle a mismatch between your Comp size/frame aspect and the exported file's size/frame aspect. If you didn't have the black borders, the resulting frame would be distorted.
Just as an example, another poster last week wanted to export from an NTSC DV Comp to a 400x300 FLV file. The problem is, 400x300 is not the same aspect as 720x480 with a PAR of 0.91 (square pixel equivalent: 654x480) . If you do the math, 654x480 and 400x300 are not the same proportions. A close match would be 400x294, for example. So, AME has to take care of the mismatch with black bars, or again, the resulting file will be distorted.
We are aware that this is confusing to users, and AE should definitely explain better what's going on, even give you options to resolve the dimension/aspect mismtatch.
If you post your Comp settings (dimensions and Pixel Aspect), and your intended frame size for export, then we can think together what would be the closest match.