It's very telling in this thread of people who have played in sports, found success in those sports, or just understands the sporting world much better than average joe mma fan.
In an individual sport like MMA the athletes are very high on themselves and in most cases rightfully so, they earned it to call the shots. It's all about what you have accomplished vs the reward of granting you the opportunity. It isn't anything to do with being scared or thinking you'll lose. It's what has your opponent done to deserve a shot against you and do you believe that they have done enough to share the spot light with you. It is all mental mentality of the athlete. It's obvious that Jones holds Stipe in a certain light as do most fans. Jones knows he could easily lose to Stipe, anything can happen in a fight. I'm not sure he takes the fight if he just thinks he'd steam roll Stipe.
It's very obvious that Jones just doesn't think Tom is worthy of sharing the cage with him at this time. Maybe Tom can get under his skin enough to change his mind and want to teach this young buck a lesson. Until Jones thinks Tom is worth his time the fight will never happen. Maybe the UFC after Jones beats Stipe offers Jones a nice bonus to fight(money never hurts in these situations) Tom and by then maybe Tom has another win under his belt and has pissed of Jones enough for him to consider it. That is probably best case scenario.
P.S.: The UFC may not want this fight. If they know Jones is done after Stipe then why would they want to risk him taking out Tom who they could just crown HW champ after Jones retires and move on instead of risking a massive mess at HW.