We can get a better view of the image from the Library of Congress page Map and views illustrating Sir Francis Drake's West Indian voyage, 1585-6, . It appears the flag in question, by its location in North America, would be a representation of a French flag.
The illustrator has simplified the image due to space restrictions, only showing one fleur, where there should be three. If we zoom in a little more we can see the disctinctive shape of the fleur-de-lis:
Images from LOC
Here is an Example of the full French flag from that era:
Update: A comment from @Jean Marie Becker points out that, due to the time frame this location is likely referencing the first French Colony attempt of Charlesbourg-Royal, -'established by Jacques Cartier in 1541'. Note the drawing of the hilltop fort on the wiki page in comparison to the map illistration depicting the flag on top of a prominent hill'established by Jacques Cartier in 1541'.
(On a side note, it seems that recent changes in my browser (Chrome) now allow full page/site language conversion with a right-click menu option. This is an extremely useful feature as foreign language wiki entries on various subjects often have much more relevant information than the English wiki versions.)