Because the A1, A2, A3 etc. radiate from London in a clockwise manner and as the motorways were built to ease congestion on these roads they were named after these A-roads. Thus the M6 travels to the North-West, as does the A6..
The first full Motorway was the M1, although the first motorway class road was the Preston Bypass which was incorporated into the M6, built before the M1