I installed Rainmeter on my computer but when I press Wind+D to see my desktop it also minimizes rainmeter
Right click on rainmeter, skin menu, position, set to on desktop. if you want to leave it at normal level use winkey+m to minimize all windows, and shift win+m to restore windows. Win+D and show desktop does not minimize windows, it draws your desktop level over open windows.
Note: if you have anything running that is not at desktop level, as myself, IconX, when you minimize windows you will not see rainmeter as you will not be at desktop level.