It makes perfect sense.

Square has the one office in SF, so essentially all of its gross proceeds arise from that office and are subject to the tax.

Salesforce has offices everywhere and a substantial amount of its revenues come from the work of employees outside of San Francisco. This revenue should not be subject to the SF gross revenues tax (and it would be illegal for SF to tax such income).

The question boils down to this: is the disparity in taxes reasonable given the SF-based gross proceeds generated by Square and Salesforce?