This does not mean that .jar files are Insecure.Several methods can be used to Protect or Pack a Jar file.Code Obfuscation is means of protecting a Java File by Complicating or Obfuscation of the Source Code.Many code Obfuscation tools are available and Smoke Screen is one of it.
Smoke Screen has a clean user Interface and Codes can be obfuscated with the click of button.You can get Smoke Screen from its official website http://www.leesw.com/smokescreen/
Now i will tell you how to protect a .jar file by using smokescreen
1)Open Smoke Screen and Select the Jar file you want to Protect by Clicking the Browse Button Next to the Source Tab.
3)Click on Start.Wait for the Process to Finish.Done! The Protected jar file can be obtained from the Destination location you specified.