Two questions:
Do you have a source for this "ninety percent" claim?
How much of the discoveries in US involved government funding?
National Review: The Drug Importation Hoax
How much of the discoveries in US involved government funding?
To answer this you'd have to understand the role our universities play in partnering with drug companies and hospitals. You'd also have to understand that much of the primary research is done in universities who are supported by grants, charity and other contributions from drug companies. Then you'd need to understand how that primary research is used by the drug companies in applications to commercialize new drugs.
Once you understand how these partnerships work you can begin to determine how a particular discovery was funded. Be aware that research today, especially at our universities, has become more about grabbing money than discovery. It's unfortunate but true. This is one of the disappointing byproducts of government trying to play a role in the process. However, if government funding of research were to stop it would seriously impact the primary research drug companies rely on.
Maybe the better question to ask is why our funding yields new drugs while others do not. Could it have something to do with the profit motive? Only a fool would think that government funding could support the infrastructure and motivation necessary to create 90% of all newly discovered drugs.