Because they have fundamentally different ideas for how much control those institutions should have over individual people. The far left (assuming communism here, which is the historical far left, though "far left" in America today is somewhat more tame) believes that all citizens should have an equitable distribution of resources, and that it's justified to compel people to work to achieve this equality. The libertarian philosophy is that people should not be compelled to do anything. One of these necessarily involves the exercise of more power by institutions.

You could look at it through the lens of positive vs. negative rights. The far left believes in positive rights (eg. the right to health care, the right to education) which require action by another party. If no party is willing to provide those services, the only way to guarantee that right is to force someone. Libertarians believe in negative rights (eg. freedom from violence, freedom from compulsion, freedom from taxation), which just require inaction. If you simply get rid of the institution, you assure the rights that libertarians care about - at least until some other institution crops up that seeks to infringe upon them. (Many libertarians make exceptions to their general anti-institutional bent to assure that no other institution crops up. For example, most support the government's monopoly on physical force simply to prevent some warlord from generating a local monopoly on physical force and using it to take away the freedoms from compulsion or theft, as long as that's the only purpose that it's used for.)