Every Muslim who is truly committed to his religion should believe of the infinite wisdom of Almighty Allah and that He is Al-Hakeem (the All-Wise). He does not order anything unwise, and yet the scholars have classified such worship acts as Ta`budi acts, which means that we cannot pinpoint one particular reason in the sense that if that reason is not there or apparent to us we can dispense with the act. This cannot be done in case of Ta`bud; they are rituals that we must fulfill regardless whether their immediate benefits, reasons, wisdom are clear or not.
The Ka’bah is the center and the focus that we are directed to turn in our prayers, and hence we should raise the slogan, “O Allah, we hear and we obey”
Moreover, Muslims by nature must believe, submit to and act according to what was authentically and duly recorded as the behavior or statements of the Prophet who said in his well-known hadith, “Pray as you have seen me praying.” If on top of this a reason or some relevant wisdom comes to light, then so be it, and all thanks is due to Allah. Otherwise, a Muslim submits to the order of Allah and His Prophet and, will accordingly, be recompensed for his obedience and good deeds.
Based on what is mentioned above, we can conclude that the Ka`bah is the place where Muslims direct their faces towards it in prayer. Allah (Sublime Be HE) is raised above being present in a certain place as there is no likeness to Him as clarified in the fatwa below. In addition, some of the enemies of Islam dissiminate that ‘Muslims kiss the stone when they prostrate and direct their faces towards an idol when they pray’, and this is a sure fallacy, and your role as a Muslim is not to be affected by such pagan claims. Your role is to seek pure and genuine Islamic knowledge through trustworthy sources and from scholars who are well-versed in Islamic knowledge. Thus, be aware and consider that your religion orders you to adhere to that which is pure, human and all things which go in parallel with the pure human nature.