Why can you only see the nucleus when looking at an onion membrane under a microscope at 40 power?

This is likely due to misleading textbook drawings/animations everyone has seen beginning in middle school.  Although the pictures do a wonderful job of showing detail for each organelle, they can be misleading in terms of their relative size.  The images give the impression that the cell is an organized, spacious place whereas the reality is that it is more like "organized chaos".  Though the processes by which cells behave and their organelles interact are beautifully complex, they simply aren't something we can observe under even 400 X magnification.

The nucleus is like a cell within the cell.  Because it is large and membrane-bound, it stains easily (with dyes like iodine) and can be quickly identified.  When you consider the field of view under that magnification is approximately 0.5 mm (microscopes can vary), an organelle like mitochondria (maximum of 0.01 mm) will just look like a dot among many other dots.