Hashem calls to Moshe from the burning bush [Sneh] and tells him (Shemot 3:5) “Shal Ni’alecha Mei’al Raglecha” [remove your shoes from your feet].

Hashem created the world as a structure with a hierarchy of species [minim: ha-domem [inanimate], ha-tzomech [vegetable], chai [animal] and midaber [verbal ] that interact in an ecosystem called aretz [earth]. The lowest is domem or inanimate objects, such as the ground. Then comes tzomei’ach [vegetable] or things that grow and
then chai or living creatures. Over all these levels is  midaber, humans who are capable of speech. At morning prayers when we thank Hashem for his blessings  we thank Him for each single blessing .However included in the list of blessings is one that thanks G-d: “SheAsah Li Kol Tzorki” that man has mastery of the world for ALL his needs  and we say this blessing when we put on our shoes!

Why do shoes symbolize: “SheAsah Li Kol Tzorki” i.e  that man has mastery of the world for his needs? When a human wears shoes made of animal hide he demonstrates that he is master over the animal kingdom .That is why we thank Hashem for individual blessings  but  also include thanks for providing us with all our necessities  with the blessing “She’Asah Li Kol Tzorki” thanking G-d for providing us with all our needs when putting on our shoes –for our needs are  symbolized by our use of shoes manufactured out of the skins of animals, By wearing shoes we demonstrate  that that Man has mastery of the world to supply his needs.

Therefore when a person wears shoes made of leather, connecting to the ground by way of the chai, this is in accordance with the world order which dictates that humans are masters over the animal species (thus we should not normally go barefoot; when a person, a midaber, treads barefoot on the ground, the domem, he is changing the order of creation see Pesachim (113b)  were it  speaks of excommunication from Shamayim for one who  walks barefoot.). . However if the ground is holy [kadosh] then on the contrary, it is our obligation to connect with it. This is why we remove the symbol of our mastery over the creation, when in a holy place –Bait HaMikdash [the Temple]and Har HaBayit [the Temple Mount]. This is also the reason that a mourner [Avel], whether for a personal loss or for a national loss such as Tisha BeAv [Fast of 9^th of Av] or on Yom Kippur [Day of Atonement], times when we are devoid of mastery over a situation, we remove our shoes. (Similarly he who refuses to perform Yibbum and do his obligation to his deceased brother by marrying his widow has his shoe removed in the Chalitza ceremony thus demonstrating his refusal to be master and take upon himself his obligations)

Therefore, Hashem tells Moshe to take his shoes off, “Ki HaMakom Asher Ata Omed Alav Admat Kodesh Hu” The ground you are treading upon is holy  .At a Holy place  one must demonstrate ones  smallness, and limitedness, and therefore makes oneself humble before God