These days it's a matter of preference as to which abbreviation to use. You'll see different people and different firms using either/or. (And a lot of people are now using "k" for thousand and "M" for million.)
If we want to get even wonkier, we could note that the English word "million" derives from the French word "mille," meaning "thousand." ("Mille" derives from the Latin, and the original Latin denotation is used to mean "thousand" in familiar words like "millennium," "millisecond," and "millipede.") The word "million" was originally invented to mean "a great thousand," or "a thousand thousand."