You can find many reasons why the Portuguese empire (and the Casa da India) failed to live up to their tasks.
Top of mind:
- Overstretching with Brazil and Morocco
- Corruption
- Ottoman attacks
- First mover disadvantage
- Partisan politics
First off, let's remember the Portuguese were the first. When the Dutch came, they mostly took over existing Portuguese strongholds, using Portuguese maps and Portuguese phrasebooks.
The Portuguese had to sink all that money in first.
Second, the role of fidalgos. The nobles were trained in the Moroccan area, in a crusade/piracy mindset, with a feodal focus on individual action. They took that to the East Indies which didn't mesh well with building alliances and big networks.
Third, it was often more profitable to do country trade than to bring stuff back to Europe, limiting the Casa's utility.
Fourth, a lot of the mercantile activities were actually handled by merchants in Anvers. So the Casa effectively handles all the risks and a limited share of the profits