Why did the Portuguese ultimately fail to establish themselves in India?

The Portuguese failed to establish themselves in India due to a combination of local wars with the Indians, particularly the Marathas and due to the rise of the British, their position in India became even more untenable. 

Compared to their Portuguese counterparts the British were well-armed and well-funded. Usually if firepower wasn’t enough, diplomacy would fill the gap. An example of this was when as part of princess Catherine Braganza’s dowry to Charles II of England, Bombay was handed over to the British. Ultimately British hegemony proved too much for Portuguese domination to become a reality in India.

For further reading check the following articles:

• Portuguese India
• British Raj
• Dutch Colonialism in India