How to use Views Isotope in Commerce Kickstart?
Views Isotope works fine with Drupal commerce. (I'm using it now =-)

Make sure you have the isotope .js file in the correct location within libraries: sites/all/libraries/jquery.isotope/jquery.isotope.min.js

also when creating the View make sure (as the above video briefly covers) that the 'Taxonomy Term: Name' in the Views Isotope filter block has the 'link this field to its taxonomy page' option turned off (5:25 time in the YouTube tutorial you posted). If it is on the links wont work.

And of course as video stresses in the main Isotope View, make sure the last field in the list is the taxonomy field that is linked to the header block. IF you need to display that taxonomy also create two fields in the view and make sure one of them is last with the correct CSS overwrite styling as the video tutorial states.

Oh and lastly, make sure your Views' Ajax option in the advanced tab is turned off. It conflicts with Isotope and wont work.