1. Pervasiveness of bad behavior. Sure, there are obnoxious BYU fans. But the numbers don't compare.

2. Degree of bad behavior. Blow-up dolls, etc.

3. Tolerance of that bad behavior by other fans. Utah fans get quite the kick out of their obnoxious compatriots and are far less willing (unwilling at all?) to step up when they see bad apples strutting their stuff.

4. Tolerance of that bad behavior by the administration. To me, this is a key difference between the two schools. Two specific incidents for comparison:

When BYU played Okie St, BYU fans shouted obnoxious stuff at Daniel Bobik for transferring away, calling him a traitor, etc. President Samuelson was so mad about it that he opened the next devotional with an angry lecture about fan behavior, informing fans that they had embarrassed the school, etc.

Compare to this incident at Utah:
http://www.cougarboard.com/board/message.html?id=8844335

Bad fan behavior occurs everywhere, but other schools do something about it. Before BYU played SDSU this year, Fisher sent out an email asking for good behavior. Some guy threw a drink at Jimmer and security was on him instantly. The Michigan hockey coach went door to door asking students to quit using lewd chants at games. Harvard cracked down on alcohol. Luck at WVU sent a letter to fans asking them to quit wearing lewd shirts. You can't stop all bad behavior, but there are certainly things you can do about it. Utah does none of those things. They just fall back on the lame "bad apples will be bad apples" line to excuse their passivity.