Our Gemara on Amud Aleph discussed a unique problem with those who do not wear tefilin:

⁦There is a category of sin called “sin with the body - Poshei Yisrael Begufan” that has an additional deleterious effects beyond the actual sin, and the punishments and judgements can be more severe. The Gemara tells us for Jews the “sin with the body” is “the skull that does not wear tefillin” and since Gentiles are also judged by God but do not have the mitzvah of tefilin, their sins with the body are that of sexual immorality.

The Gemara uses an odd phrase to describe this person as a “skull that does not wear tefillin”.  Why not mention the tefillin on the arm? And, also why the “skull”?   And, how does it make sense to equate a Jew not wearing tefillin to a Gentile committing sexual immorality? Ben Yehoyada explains that the Shel Rosh is the revealed part of the Tefilin and wearing or not wearing is a defacto declaration of acceptance of the yoke of heaven or rejection, and for a Gentile, being sexually immoral is also a casting off of the yoke of heaven . 

This answer does not feel satisfying, as there seems to be more going on here with this choice of words, as well as the equating of tefillin to sexual immorality.

Rabbenu Yonah Shaare Teshuva (3:11) implies a partial answer.  The constancy of ignoring a daily commandment accrues and accumulates in a toxic manner.  He also implies that it is not so much the mitzvah of tefillin, but any positive commandment that is daily and ignored.  Based on this, I would like to suggest the following deeper explanation, which might be partially what Ben Yehoyada meant.  

There are problems or states of thought that operate on a continuum. For example, if one shows lack of gratitude to a parent in a mild state, we can easily see how that character deficiency can over time escalate into full-scale narcissism and disregard for any authority as well as lack of empathy.  Does it mean that it will lead there for sure?  No.  But, we can understand how it could lead there.  The description of the sin of the body of the Jew versus the Gentile is a metaphoric description of the sin of the smallest scale manifestation to the largest scale, but on the same continuum.  Thus, the lack of ability to accept upon one’s intellect the yoke of heaven on a consistent basis will lead to further deterioration, which at its most severe stage is sexual immorality.

Checking in with God daily through the mitzvah of tefillin is indeed an important protective factor for all levels of observance and so I will speak about this for a bit. I have noticed a sociological psychological phenomenon amongst a segment of the population.  Certain otherwise observant people do not wear tefillin. From anecdotal evidence, it occurs with greater frequency than other lapses.  Individuals who otherwise observe kashrus and shabbos still seem to have difficulty with tefillin. Many depressed or disenfranchised adolescents also let their tefillin gather dust, to the anguish and distress of parents whom, filled with optimism for the future, spared no expense in getting the most mehudar tefillin. Logically, it is perplexing because tefillin as a mitzvah can be performed in approximately one minute, and if one adds reciting the Shema, it would take all of five minutes.  Feelings are not logical but they still follow understandable pathways, so we must ask what seems to be behind “tephiliphobia” and what can we do for those who express a wish to overcome it?  

The observance of the tefillin ritual is powerfully symbolic.  As stated in the writings within the parchment that is being worn inside, it represents acceptance of the yoke of heaven on the arm and on the head, or the heart and the mind.  It also is the mitzvah that a young man begins to observe as he approaches Jewish manhood. All these meanings must come to a painful clash when a person has difficulty with religious observance.  In a way, it can be seen as a positive sign of integrity, that the person cannot bear to enact acceptance of the mitzvos when he feels insincere about it. From a halachic point of view, this integrity is misplaced, but it still is significant.  

Another aspect of Tephiliphobia is all or nothing thinking. Since Tefillin are associated with prayer, as their Hebrew name suggests (Tefilla = Tefillin), some may find it difficult to wear tefillin when they cannot pray.  Prayer is much harder and much more time consuming, but for some these two independent observances are inextricably linked.

If a person wants to wear tefillin but becomes anxious, avoidant or resentful when trying to do so, separating the strands (or straps!) may be helpful.  What are the negative associations with the tefillin? Are they being lumped together with prayer, even though they can be seperate? Is the feeling somehow linked to uncomfortable associations with the Bar Mitzvah or teenage years?  

Another helpful intervention is to personify your tefillin and imagine, or even write out a conversation you would have with them.  If your tefillin had a voice, what would they say to you?  What would you say to them?  It is time for you and your tefillin to have a heart to heart talk.