In 1635 Charles I had established a competitor to the East India Company, the Courteen Association. Though this wasn't successful, it was one factor that caused the Company to generally support parliament (though there was extensive internal division and argument within the organisation, but as Parliament gained dominance, so did the Parliament faction within the Company).

There was a view of several Commonwealth leaders that the Company's monopoly represented the sort of despotic rule that they had fought to end. However, it was allowed to continue for the deeply pragmatic reason that it was a useful source of funds to the republic through forced loans.

The Company's charter was due for renewal in 1654, Cromwell decided in 1653 to not renew the charter, which led to a shambolic and unprofitable free-for-all in East India trade (to paraphrase Lawson).

By 1657, pragmatism won over ideology and Cromwell granted a new monopoly charter to the Company. This charter has been lost, but is considered to be very similar to the 1635 charter. However, it established the first permanent joint stock in the Company, which Hunter argues represents the transition to a modern basis of management.

Sources:

Lawson - "The East India Company: A History"

Hunter - "History of India: Vol VII"

Riddick - "The History of British India: A Chronology"