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I'd say for that purpose r-trees are more suited than kd-trees, but yeah. From what I've heard, it's very much standard practice to use r-trees or other structures for collision detection in game engines where you have a very large number of entities/surfaces/etc which you may want to perform collision detection with.

With regards to 'other structures', so long as things are in a bounded size region and the density variation of objects is not too extreme, rather than a tree you'd probably get better results taking a very simple approach: Divide the area into a 2d grid, scaled so that you have a no more than a few entities in each cell, and in each cell store a list of entities which are within that cell. The only reasons to use a tree instead of a coarse array, is when the density of collidable objects/surfaces varies significantly between areas (i.e. you don't want lots of cells that are near-empty with other cells that have thousands of objects)