It is by no means right to say that Nixon's presidency had only negative effects. However, his time in office is remembered mostly in negative ways.
Nixon's presidency had a negative impact on the country mainly because it did so much to erode the trust that Americans had in their government. Before Nixon, no American president had openly broken the law and openly lied to the American people about what he had done. When Nixon did this during the Watergate scandal, it accelerated a trend that had already been started by Nixon's actions (and those of Johnson before him) and statements with regard to the Vietnam War.
The main negative impact of Nixon's presidency, then, was to help destroy Americans' faith in their government leaders. We continue to feel the effects of this loss of faith today.