Short answer: Yes.
As long as the cable is an ethernet cable with RJ45 connectors and NOT a cross-over type cable, a Cat 6 cable will work the same as a Cat 5 (or Cat 5e) with your MFC-101 and Axe-Fx II. Cat 6 cables are generally more rigid and less flexible than Cat 5 cables due to an extra “spline” separator and usually thicker wire, so they may not lay as neatly on the ground as a Cat 5.
See this post to read more about ethernet cables: Ethernet vs etherCON – Cat 5 vs Cat 5e vs Cat 6
See this thread on the Fractal Audio Forum: http://forum.fractalaudio.com/mfc-discussion/95407-cat-6-ethernet-cable-mfc.html#post1142426