Mythology holds that Lord Shiva once cut off the 5th head of Brahma. Thirumular's Thirumanthiram states that Lord Shiva holds the skull cap of Brahma as a begging bowl in order to save it from hitting the earth and perishing, for Brahma is the creator of the Universe and his head signifies all that lives and transitions to the next life after death. Lord Shiva is also known to wear a garland of skulls that belong to great celestials, as he protects them from falling to dust. Hence the idea of holding the skull cap and wearing a garland of skulls has a very profound meaning and is not as gory as perceived by many.
These are not just stories as they hold a great deal of truth and deeper significance and this brings us to the larger question of why is a skull cap a significant depiction of a begging bowl?
Lets take a few steps back and observe another ancient tradition, that of Buddhism. The idea of ahimsa as well as the idea of bhiksha started during the time of Buddha. There is great significance to the begging bowl in Buddhist tradition. When Sidhartha Gautama Buddha reached the end of his journey to enlightenment, he realized his emaciated state was of no help and that he would need food to gather the energy to go through to the other side. It was at this time that a young girl gave him grain in a golden bowl which he divided into 19 parts, one for each day till the day he reached his moment of enlightenment. One he crossed the threshold to the other side; he discarded the golden bowl into the river - a marked significance of detachment from any kind of materialism. The golden bowl marked the catalyst to Sidhartha's transition from one state to the next.
Ancient faith believes that the last segment to divine Nirvana is when the Kundalini energy reached the highest zone, that which is near the Kabala of the human skull. It is also believed that Jeeva enters the body through the Kabalam and if it exits the same way, one is blessed with superior transition at the time of death, it is the perfect death achieved.
Brahma, the creator symbolized the transition of life and death in the hands of the Lord of destruction. Hence the passage of the afterlife and the highest form of realization is depicted through his kabala which is held as a skull cap, a bowl that depicts the last state before one attains the highest form of spiritual bliss.
Both Buddhism and Hinduism tried to depict this great truth in their own ways. While Buddhist belief took a different turn and depicted this truth in a far less violent way, ancient Tantrik cults and Vajrayana Buddhism depicted the ferocity of Kala Bhairava, the Lord of time in their depictions by emphasizing on the skull cap which symbolizes the Bhramaranda zone of the skull, where the essence of Atman remains shrouded in this area and releases the soul upon death.
Such deep significance of life and transition to super death, such profound truth lies embedded in what we perceive as just a skull cap in the form of a begging bowl.
P.S. It would be interesting to note that the Tibetan Buddhist tradition has also devised a singing bowl which reverberates the sound of OM when one plays it while meditating. Could it possibly signify the highest state of bliss when the mind resonates the primordial sound of OM.