Why did Mercury not appear to transit through the middle of the sun? Why did Mercury not appear to transit through the middle of the sun (the equator)? I initially thought that this was because of the ecliptic, but, then I thought that actually we'd see it above the solar equator, wouldn't we? So I'm confused. 

This video of the transit from NASA shows exactly what I'm talking about. Mercury is shown relatively low on the solar disk.

I'm looking specifically for why it was visible in the bottom half of the sun, not the top half?
Mercury's orbit is inclined 7 degrees relative to Earth's orbit.

This drawing is exaggerated. When Mercury is "between" us and the Sun it might be below, above, or passing through the Sun's disc from our point of view.



Another post from Universe Today explains this also.