Since factom is a private company, are they applying for patents on any innovations they are making on the current blockchain technology or are other companies free to copy their innovations? I feel this is important for investors to know before they invest in the company or factoids the currency.

If they have patents and their innovation are useful than we are taking about a billion dollar company, if it's open free for all to copy and use, I think in terms of financial returns for investors might not be much. The company could still be a success but chances for exponential growth might be less.