Wiring a ceiling fan with different wires from the ceiling
This deal is sorely in need of some colored electrical tape.  Seriously.  

There is one /3 cable (black white red) since ground is not counted as a conductor.   It is the same cable both in the fan box and the switch box.  On this cable: 


Mark both ends of the white wire with black tape, to designate that it is for "always-hot".  Use of the white wire for always-hot is mandatory in this case, but also mandatory is the marking I just described.   This is the only mandatory marking; the rest a done for sanity's sake.    
You see in the switch box where the white wire joins a black and red wire in a wirenut.  They are both short pigtails, also mark the red wire with black tape near each end, which will reduce confusion in that box.  
The red wire exits the cable in the switch box, and hits a wirenut to connect to a red pigtail that goes to a switch.  We'll leave that all red.  
The black wire exits the cable in the switch box, and hits a wirenut to connect to a red (!!!) pigtail that goes to a switch.  Annoying!  So we will: 
get blue tape, and on the /3 cable, mark both ends of the black wire with blue tape.  Also mark the red pigtail with blue tape.   


Ok, now counting the tape color, black = always hot, blue = switch 1, red = switch 2 and white is neutral.   This just got a whole lot easier.  

Up in the fan box,  black gets nutted to black (which is the white wire remarked black, and NOT the black wire remarked blue).  

Three wires remain: blue, red and white which is actual neutral.   That is what your fan needs.