Could be any of the following explanation, or a combination of them.
- Government takes bribes from the company
- Company convinces everybody that aid to terrorists came from a "few bad apples", i.e. a small group of employees that do not represent the entire company
- Company is too important, both for medical innovation, and manufacturing of medical drugs and equipment, and employing the thousands of people. The management of the company is jailed, along with whoever knew about terrorists, but the rest of the company continues to operate under new management (and increased government oversight). They could break the company up, and sell its facilities to other medical companies, but the goal will be to preserve the research and manufacturing operations, since they take a lot of time and money to set up properly.
Edit due to updated question So the premise is that your protagonist found about terrorist funding, but broader government does not want to do anything about it? The reasons above still apply, but here are some more reasons.
Government might be waiting for legally acceptable proof. If your protagonist obtained proof through illegal means, it is not admissible in court. From gov't perspective, your guy could be one criminal trying to get rid of another.
Some faction in government benefits from terrorists, e.g. as justification for military spending, or b/c terrorists are "enemy of my enemy". US, Soviet Union, Iran have all sponsored terrorist groups that targeted their enemies.
Now for what your guy can do:
- Cut off financing - requires access to banking authorities.
- Expose the whole thing, in press if evidence is too weak courts.
- Blackmail the CEO or whoever is giving money to terrorists.