This is a controversial topic. The fact is that the KKK is able to meet and be protected under the law. The first amendment provides freedom of religion, speech, and the press. So, all people and groups have a right (under U.S constitutional laws) to express themselves and to assemble. We will get mileage by looking at the issue historically and in the reverse.
Historically speaking, there were various minority groups that were unpopular such as women's rights and the outlawing of slavery). Imagine if they were not able to meet. To put it another way, by allowing minority groups to meet, you have a mixed bag - both good and bad groups. The greater problem would be if the government decided who can and cannot meet.
If we think about the issue in the reverse, it can be helpful. Say a few members of the local Baptist church committed a crime and people wanted to shut not just that Baptist church down, but all churches, there would be an outcry.
Based on these points, the government still allows the KKK to meet.
With this said, there have been times when the government intervened. The Ku Klux Klan Act of 1871, as well as the Enforcement Acts of 1870 and 1871 sought to prohibit the use violence and intimidation. But on the whole, the Supreme Court allowed the KKK to meet. Brandeburg v. Ohio, a watershed decision, in 1969 ruled that the government cannot punish inflammatory speech, unless that speech is directed to inciting violence or imminent lawless action.
In conclusion, the government has taken a middle of the way approach with the KKK.