Of course with any change you also have the flip side. Time will tell how these open borders will shift the paths for drug trafficking and illegal immigrants making their way to Western Europe. Also, now that Slovakia occupies one of the EU's easternmost boarder with non-EU Eastern Europe (primarily the Ukraine), security concerns are of top priority to maintain the integrity of the EU. Just two weeks ago Slovak police caught a group of Hungarian/Ukrainian arms dealers trying to smuggle in uranium. Despite all of these concerns, the hope is that the benefits will outweigh the inescapable drawbacks.
If you would like to learn more about Schengen check out: http://en.wikipedia.org/wiki/Schengen_Agreement