Adam Clarke on Psalms 99:1

The Lord reigneth - See the note on Psa 97:1.

Let the people tremble - He will establish his kingdom in spite of his enemies; let those who oppose him tremble for the consequences.

He sitteth between the cherubims - This is in reference to the ark, at each end of which was a cherub of glory; and the shechinah, or symbol of the Divine Presence, appeared on the lid of the ark, called also the mercy-seat, between the cherubim. Sitting between the cherubim implies God's graciousness and mercy. While then, in his reign, he was terrible to sinners, he is on the throne of grace to all who fear love, and obey him. Though this symbol were not in the second temple, yet the Divine Being might very well be thus denominated, because it had become one of his titles, he having thus appeared under the tabernacle and first temple.