I think you've given your son good advice, based on the information you've shared in your post. To help determine whether the school refusal stems from inappropriate behavior on the part of others which rises to the definition of bullying, from your child's sensitivities, or some degree of both, you may wish to work with him on describing each incident in observable, factual terms (who, what, when, where, how), and possibly keeping a log.
It is my understanding that assessing "why" would be considered conjecture and not an observable fact.
It is also my understanding that not all exclusion or negative commentary rises to the definition of bullying, but rather that the negative treatment must be a repeated pattern, after being told to stop.
Some children may be missing social cues which others pick up on, or may have quirks which may tend to unknowingly send a body language message that raises red flags, even possibly signaling that they prefer to be alone. Different parents have varying views on teaching social awareness and/or instructing others to accept their child's "quirks".
Resources on social teaching, on anxiety, and on bullying are found in a number of threads on the forums. Here is one resource-y
post which may be of interest. Developing healthy interpersonal
boundaries may also be of interest.