This is because Allah is truly with us and is truly above the Throne, as Allah, glorified and exalted be He, brings both together in His words:

“He is the One who created the heavens and the earth in six days, then rose over the Throne. He knows what enters the earth and what comes out of it, what descends from heaven and what ascends into it. And He is with you wherever you are. And Allah sees all that you do.”

Thus, He states that He is above the Throne, knows everything, and is with us wherever we are. Likewise, the Prophet, may Allah bless him and grant him peace, said in the hadith of the mountain goats:

“Allah is above the Throne, and He knows your circumstances.”

This is because, when used without qualification, the word “with” signifies in its apparent linguistic sense only association in general, without necessarily implying contact or being alongside something to its right or left. When qualified by a particular meaning, it signifies association in that respect.

For example, one says, “We continued travelling, with the moon with us,” or “with the star with us.” One also says, “This baggage is with me,” because it accompanies you, even if it is above your head. Thus, Allah is truly with His creation and is truly above His Throne.

What this “being with” entails varies according to the context. When He says:

“He knows what enters the earth and what comes out of it,”

and continues to:

“And He is with you wherever you are,”

the apparent meaning of the passage indicates that what this being with entails and implies is that He observes you, bears witness over you, watches over you, and knows you. This is what the early generations meant when they said, “He is with them through His knowledge.” This is the apparent and actual meaning of the passage.