I had a similar problem with my Surface Pro. I had it inside a sleeve in my backpack with the cover closed, and came home to find it very warm and the battery nearly drained. I found this useful website which has a number of troubleshooting steps for this kind of issue:
How to prevent your PC from waking up in sleep mode - PC Advisor
After reviewing the entries in the Event Viewer, I found that about every 3-5 minutes, my Surface Pro was waking up with "Wake Source: Device -USB Root Hub." As I went through the Device Manager, for the USB Root Hub entries, under the Power Management tab the "allow this device to wake the computer" was grayed out. However, I figured this entry could be secondary to some other event on another device, perhaps the keyboard, trackpad, etc. as has been suggested in other posts. What I decided to then do was to go through EVERY device in the Device Manager, check the Power Management Tab, and whenever available, uncheck the box for "allow this device to wake the computer." For example I did this for the type cover, for the mouse, etc. This may sound tedious but it just took about 5 min.
With these settings modifications, the only way to wake up the Surface Pro is 1) Press the power button briefly or 2) Press the Windows button on the screen. I think this is pretty easy and much more reliable than never knowing if your Surface Pro will wake up spontaneously.
Since then, my problem seems to have been solved. In my power options, I do have enabled the settings to sleep when I close the cover. This works properly, so when I want to put the Surface Pro in my bag, I just close the cover. But now when I take the Surface Pro out of the bag, it is off as expected. If I open the cover, it stays off, unless I press the power button on the top or the windows key on the screen. If I press anything else (keystrokes, touchpad, etc.), then the Surface Pro does not wake up.