Foods that digest quickly (most fruits) should not be eaten with foods that will have to stay in the intestinal tract longer (proteins, such as beef, chicken, pork).
The book Alkalize or Die, by Dr. T.A. Baroody, suggests eating fruit at least 20 minutes prior to eating other foods to allow the fruit to have a head-start on the system.
Heavy meat/protein foods mixed with fruit can slow down elimination and cause the fruit to putrefy (rot) which sometimes result in foul burps, excessive gas, and food hardening in the lining of the intestines which ultimately may be the cause for some diseases.
I agree with "personaltraining", I have been taught that protein and carbs combos actually constitutes a basic meal and should be eaten together.
Certain foods and fruit juices can assist in releasing nutrients in other foods. If I take an iron pill, I drink orange juice which is a good binding agent.