If you want to use auto-tax, add the -loyalty switch to your VI shortcut properties. You want to set the level to 120 or 130, 100 doesn't take certain things into account and leads to surprise rebellions.
Code:
"C:\games\Total War\Medieval - Total War\Medieval_TW.exe" -loyalty:120
This will also affect the AI taxation levels, which leads to a better game in general. The AI factions don't collapse as easily and tend to build better garrisons.