All the comments you have received are right on. The first thing to ask is what are your goals with him? Then, are your goals realistic. Then, what are you doing to achieve those goals, and what are you doing to make those goals more difficult to achieve.
You do not provide enough information to answer some of those questions, so the following comments may or may not apply to your situation.
I hope your goal is to simply have a monitor that tolerates your presence and does not mind some interaction. Setting your goals higher than that often leads to disappointment. That is not a rule, but most monitors do not learn to "enjoy" your presence. Oftentimes, the more we attempt (more like force) to get them to enjoy us the more they fear (that is what those reactions represent: fear) us. Work on that basic goal and adjust your goals when you achieve that point, or adjust down if your animal never acclimates to that point. You might get an animal that appears to enjoy your presence. You might get an animal that despises you. Your behaviors now can influence the end result greatly, but you must also accept the animal controls that on its own as well.
Right now you are holding the 2 foot animal in your hands and rubbing him. Essentially you are forcing him to put up with your contact regardless of what it wants. That works sometimes (and I am sure there are people here for whom that method has worked). However, what usually happens is that either they become tolerant of this type of interaction or they become very ill-tempered animals that fight at every opportunity to get away. Lots of animals end up fitting the latter description, moreso than the former.
In my experience, rubbing is an action they learn to accept much later after initial trust is gained. Babies "tolerate" it because they are too small to fight you and when you stroke them they figure they are dead and do not bother fighting (they give up). Older/Larger monitors fight back in proportion to their size. I do not know what goes through a monitor's head or what insticts being rubbed triggers, but most of them do not seem particularly fond of this activity. I would suggest that touching them on their neck is a danger trigger for them (most animals do not like you near their necks when you are the size of a predator). Touching their legs, arms, and tails seems like a predatory assessment to disorient them (ever see how predators fling their prey about? Arms, legs, and tails make great instruments for subduing prey). It might feel good if their skin is dry or something is bothering them like an itch or if they are cold (and you are warm) or if they are one of the few that learns to enjoy it.
Most monitors learn to tolerate it because they trust you enough to know you are just going to annoy them a little bit and then leave them alone, similar to a compromise: if I let him pet me now, then he'll leave me alone later or he will feed me.
You have to accept that you are still a predator to this animal, especially if you have been interacting with him like this since he was a baby (and I suspect you have based on your post). 3 months and 2 feet is not nearly long enough to have established trust or any sense of your benevolent intents in his life.
You have made one conclusion that is very noteworthy: he seems to be more frightened. He probably is. So, my advice is to leave him alone. Establish a pattern where you feed him and he can associate the big predator (you) with good things (like food). As you establish this connection, he will fear you less and avoid you less. You can then attempt to pick him up or touch him (again, I'd avoid stroking him) in his world (enclosure). When he tolerates this contact, then you can move on to picking him up and interacting with him in your world (outside his enclosure). You might even get to a point where you can pet him and he will let you do so. You might have to settle for less.
One final piece of advice: do not violate their hide spot without a very good reason. They really hate (fear) having a home they think is secure and then suddenly it rises off of them and a predator appears.
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^x^ Bloodbat ^x^
Monitors, monitors everywhere
and all the food they ate.
Monitors, monitors everywhere,
their parents loved to mate.