Are you using a proxy? Can JBDS connect to other sites (for example on the Central page, can you see the RSS feed) ?
If you have some specific connection settings to use, you can configure them as explained there http://help.eclipse.org/kepler/index.jsp?topic=%2Forg.eclipse.platform.doc.user%2Freference%2Fref-net-preferences.htm
What version of Oracle java are you using ? See today's post about the regression error in update _40 of java 7. You may want to revert your java to java 6 until java 7 is error free. Btw, I recommend using the 32 bit java instead if you are running on windows.
no need to revert to Java 6 - just avoid the _40 update of Java 7
Most likely cause of this is as Mickael suggests, a proxy issue.