The "R" that Roger is substituting for stands for received, indicating that a radio message has been received and understood. The use of radio-alphabet terms to stand for other words is common in the military; roger is a well-known example, and another example is Charlie referring to Viet Cong troops, which comes from Victor Charlie, a radio-alphabet spelling of VC for Viet Cong. "Wilco" is not from a radio alphabet; it's a military abbreviation for will comply, indicating that a message that has been received will be complied with. It's necessary to acknowledge receipt of a message with Roger before indicating compliance with wilco, hence the frequent combination Roger, wilco.
Both Roger in this sense and wilco appear for the first time during World War II
from:
http://www.randomhouse.com
