Were the vertical stripes used to contrast or protest the British East India Company flag that had 13 horizontal stripes? Probably not. But it's not really clear.

We do know that the first American flag adopted by the Continental Congress, the Grand Union Flag, was based directly on the East India company's. Honestly, it simply was the East India Company's flag, but slightly truncated. The British East India Company had complementary interests in ending the Stamp Act as the Sons of Liberty, so it could have even been a sly public relations gimmick to tie in powerful business interests to the tax protest. That's just conjecture, however.

Once the Crown outlawed the vertical rebel stripes entirely, some accounts say that the Sons of Liberty started using a horizontal version that had thirteen stripes just like the British East India Company's flag, so something may have been connected somehow. Though in truth, many of the flags may have also just been British Red Ensigns defaced in protest as contemporary accounts may suggest. 

Whatever the case, the Sons of Liberty Rebel Stripes Flag is a wonderful symbol of American resistance, independence, and patriotism.