The Counterculture challenged the conformity which had marked the 1950's and for that reason was considered abominable by the mainstream populace. When one considers its long term consequences, however, it probably did produce both good and bad effects.
The good effects were that people no longer accepted the status quo. Women gained new rights and were accepted as equals; conformity was no longer considered the norm, in fact free thinking and challenging accepted standards became popular. Although it seemed unthinkable at the time, it required many Americans to re-examine their own standards. The Counterculture also forced people to re-examine the role of the United States in Vietnam and also lent itself to the environmental movement.
On the flip side, the counterculture did lead to the recreational use of drugs and removed the stigma previously attached to casual sex. This was perhaps the cost of the benefits which arose from the counterculture.
This is, of course, completely a matter of opinion. I wish that we could have gotten the "goods" that came from the counterculture without the "bads." However, all told, I'd have to say that I think that the goods outweighed the bads.
To me, the major good that came out of the counterculture was a greater amount of equality for women. If you include the Women's Lib movement as part of the counterculture, you can see that the counterculture gave us a society in which women go to college as much as (or more than) men and in which women and men are coming to have nearly equal status in society. The bads of the counterculture are generally things that people can avoid if they want to. You don't have to subscribe to the ideas of "sex, drugs and rock and roll" if you don't want to.
That is why I think the goods outweigh the bads. The goods are things that apply to everyone (or at least all women). The bads are things that you don't have to accept. That means that everyone can enjoy the benefits of the changes brought by the counterculture while not everyone has to suffer from the bads.