First of all, their decisions should be focused on the needs of the organization, not the personal interests of the founders. That's why, in many states, it is required that a minimum of three people serve on a not-for-profit board, whereas a for-profit company may be owned and managed by as few as one person.
Second, founders don't have the legal right (simply because they are founders) to be as autocratic about directing the operations of an organization and insisting that it take a particular route. Whereas the founder of a for-profit corporation would certainly have more sway.
That said, founders have the practical ability to vote with their pocketbooks, as do any other major donors. If the founders don't like the direction in which the organization is moving, they have no legal obligation to continue their financial and other support.
It can be difficult for founders to relinquish control of their "baby" for a number of emotional reasons, including their need to feel needed and important.
It may be worth the investment in a consultant to help facilitate a conversation so that all sides can buy into the shift in roles that have occurred.