Colonel Harold Malet, in Notes and Queries, August 6th, 1892, p. 116, says that “John” is a perversion of “Hon.,” and John Company is the Hon. Company. No doubt Hon., like Hans, may be equal to John, but probably John Company is allied to the familiar John Bull. The Company was abolished in 1857, in consequence of the Indian Mutiny.
“In old times `John Company' employed four thousand men in its warehouses.” —Old and New London, ii. 185.
Source: Dictionary of Phrase and Fable, E. Cobham Brewer, 1894