Milk interferes with the rate of absorption of certain medications in the guts. Antibiotics especially tetracycline are greatly affected if taken with milk. The calcium in the milk binds to the antibiotics and this prevents the absorption of the medicine in the gut. The medicine has no effect on the body because it is been excreted out of the body.
However, certain medicines are adviced to be taken with milk. Medicines like Aspirin and other non steroidal anti-inflammatory drugs. This is to prevent the damage this drug can cause to the stomach lining.
Milk does not affect the absorption of many drugs except for special cases like the one above.