Some Johnsons may actually be MacGregors !
In early times, the city of Perth> was called St John's Toun (the local football team is still called St Johnstone) and when surnames became more frequent, many of the people from there took the name Johnstone.
When the MacGregor name was proscribed (banned) a number of that clan took the name Johnstone.
http://www.rampantscotland.com/timeline/1899.htm
offers the reason for the banning of the MacGregor name
also see