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A summary of what’s known, for my own reference:

1. Diphenoxylate inhibits excessive GI motility and GI propulsion; commercial preparations contain a subtherapeutic amount of Atropine to discourage abuse
2. Antiperistaltic agents should not be used in these conditions:
   • diarrhea associated with organisms that penetrate the intestinal mucosa (toxigenic E. coli, Salmonella, Shigella)
   • pseudomembranous enterocolitis associated with broad-spectrum antibiotics
3. Diphenoxylate action begins within 1hr, peaks at 2hrs, lasts for max 4 hrs.
4. Atropine is a competitive antagonist of the muscarinic Ach receptors. Because Ach is the main neurotransmitter used by the parasympathetic system, this blocking of its pathway of action, reducing digestive action related to salivary, sweat, and mucus glands that rely on Ach action.
5. While Atropine is included to prevent abuse, the secretion-reducing effects of the atropine can aid anti-diarrhea effects of Diphenoxylate.

Sources:

1. http://ibdcrohns.about.com/od/prescriptiondrugs/a/lomotilfaq.htm
2. http://www.umm.edu/altmed/drugs/diphenoxylate-atropine-043900.htm
3. http://www.rxmed.com/b.main/b2.pharmaceutical/b2.1.monographs/CPS-%20Monographs/CPS-%20(General%20Monographs-%20L)/LOMOTIL.html
4. http://www.rxlist.com/cgi/generic/diphenoxylate_wcp.htm
5. http://en.wikipedia.org/wiki/Atropine