Drugs which are given orally are most often absorbed by either the stomach or the intestine; most drugs absorbed by the intestine are absorbed by the small intestine rather than the colon, and very few by the rectum. It is the small intestine which has much larger surface area and "active" transporters designed to move larger molecules like those of vitamins and medications into the blood stream. See also http://dmd.aspetjournals.org/content/31/12/1507.full .

A typical abdominoperineal resection (APR) removes just the rectum and anus, with perhaps a small amount of the distal colon. The resection itself should not cause difficulty with absorbing medication. However, it is (theoretically) possible that the disease or surgery could be associated with other problems that may cause food and medications to go through your GI tract ( http://wiki.medpedia.com/Digestive_System ) too quickly. Do you have such issues as frequent diarrhea or seeing food or pills pass in your stool unabsorbed?