In the next phrase, Jude gives background on these certain men, mentioning that they were "before of old ordained to this condemnation". Since men have free will, and God is willing that all should come to repentance, this is not the Calvinistic belief of predestination as they see it. Rather, it is seen through a long line of prophecies and examples about certain men such as these, who were "marked out for" condemnation. These certain men were "long ago marked out for condemnation". Though they may be indistinguishable at times now, in the end their destruction is very clear. Peter says that they will "bring upon themselves SWIFT destruction", because they themselves are deceived along with others. Jude in the following verses gives several examples of groups who were similar to these certain men, and in verse 8 begins "likewise...".
The application: Just as those in the past were destroyed for their sin, these certain men are also ordained for destruction. In the parable of the wheat and the tares, Jesus serves to warn the laborers of the field about the tares that Satan has planted. A warning sign is that they bear no fruit. Whether we can recognize them or not, Christ knows who they are. Nevertheless, He lets them grow until harvest, or Judgement, when He has the angels separate them from the wheat and casts them into a pile to be burned (Mat. 13:24-30, 36-43). Jude's brother and Master, God incarnate, says that we will live with these tares, these certain men, but in the end they will be judged accordingly.