In order to get Kodi to not assosiate .zip to music/video you got do an edit to advancedsettings.xml.
nano .kodi/userdata/advancedsettings.xml
<advancedsettings>
<videoextensions>
<remove>.bin|.img|.iso|.zip</remove>
</videoextensions>
<musicextensions>
<remove>.cue|.zip</remove>
</musicextensions>
<pictureextensions>
<remove>.zip</remove>
</pictureextensions>
</advancedsettings>
Hope this helps you.