You can try vectorizing that code, but that will be most likely destroy any short-circuiting you have in there.
Just by the top of my head, following code should be able to replace your for-loops:
brighterThanBg = (im > bg + tol);
darkerThanBg = (im < bg - tol);
outIm = (brighterThanBg | darkerThanBg);
That will also check every pixel but it will be faster as MATLAB is quite slow on loops. Also, by inverting your logic (you check for background, split into 3 regions, 2 of which require 2 conditions to be satisfied), while this codes only takes care of 2 regions (pixels too bright to be background, pixels too dark to be background), each only requiring a single condition.