For a 2D, top-down view, the natural ordering of a tile map is a linear array, organized as a 2D matrix. The coordinates of any given tile can be calculated by `y * width + x` (row-major) or `x * height + y` (column-major). Conversely, you can calculate the x and y from the index of a given tile.  This is not the only way to represent such a map — for example, if you have an extremely large map it may be worthwhile to ‘swizzle’ the array, storing blocks of tiles sequentially rather than entire rows. 
The advantage of the top-down view is that order of rendering is less important. Tiles do not overlap, so the order they are rendered to the screen does not affect the final image. Therefore, rearranging the tile array has no visible effect on rendering. The matrix view of the map is easy to reason about, so this is convenient.
An isometric view, on the other hand, is a different matter.