This is a setting within the program itself really easy to disable, I disabled it too as it got annoying.
Here's how to fix it(Assuming you are using windows);
1. Open Skype
2. Navigate to tools tab at the top of the program (or use ctrl+,).
3. You should see a screen pop up, make sure at the side of the new window 'General Settings is in blue'
4. On the right-hand side there is a number of settings with boxes at the start, find the third one down that says "Start skype when I start windows"
5. Uncheck the box then press save at the bottom right side.
6. That's you done.
Now the next time you turn your computer on it shouldn't open
Hope this helped
Lewis W