What did Hashem mean when He said "Hinei Makom Iti"?
Rashi #1: He meant that there was a designated spot on the mountain where He always spoke to Moshe, where He would conceal him, so that he should not come to grief when He passed. 1
Rashi #2 (citing Midrash): Hashem was pointing out that He was the location of the world, and not vice-versa.
Ramban: There is a designated location on this mountain where My Shechinah is located.
Seforno: He meant that He had a specific location that was designated for the revelation of the Shechinah. 2
Avos de'R. Nasan, Perek 12: The location referred to by the Pasuk is the portion of Moshe Rabeinu that was reserved for him since the six days of the creation. 3
Why did Hashem initially instruct Moshe too stand on the rock and not inside the cave?
Oznayim la'Torah: I seems that there was no cave there to begin with and it was only when Hashem's Kavod was about to pass that a strong wind that was capable of 'uprooting mountains and smashes rocks' bored the cave into the mountain.
