I have just finished and signed the apk through android studio, then I have did an apk protect through apkprotect.com when I am trying to upload the apk to play store I go
I got the same "You uploaded an APK that is not zip aligned... blah, blah" error when by mistake I tried to upload a DEBUG version of my .apk file to Google Play. It's a bit misleading error because the real problem is that you cannot distribute a debug version which additionally is not signed with your Google Android Developer key. (You can only upload an .apk compiled as release version, and it must be signed, which happens in the same step, at least if you're using Eclipse).
Make sure you distribute an .apk file which is your Signed Release version, as described here:
http://developer.android.com/tools/publishing/app-signing.html#releasecompile