Hi Paul,
One way to make the background transparent is to apply the Color Key filter (in Filters>Keying) to the fire clip, then use the eyedropper to sample the black. This will tell Motion to “key out” (remove) the black parts of the clip and let the layers underneath show through. Once you’ve done this you will probably want to tweak the result, either by adjusting the Tolerance slider, and/or adding the Matte Magic filter as well.
Alternatively, depending on the precise effect you want to achieve, you could apply the Luma Key effect instead of the Color Key, and set it to Key Out Darker.
Even more alternatively, you could forgo any filters altogether and try simply setting the Blend mode of the fire clip to something like Add, Lighten, Screen or Color Dodge. Any of those will drop the black background out and composite the fire clip onto your background, although each will give a the resultant composite a different “feel”.