I haven't seen any touch-typing tutorials myself that really give much credence to the modifier keys. Of course, I learned to touch-type properly some ten years ago now and have been using computers for much longer than that, which may influence things a little.
In the end, all of touch typing boils down to what you find comfortable. There is no One True Way, except that typing should be comfortable for you. Comfort reduces body stress as well as likely reduces the number of mistakes you make.
What I do, which works well for me, is to keep my hands mostly in the home row position, or near it (I will often rest my hands to the sides of the alphanumeric part of the keyboard). As a result, for me the modifier keys are at:
Caps Lock and Left Shift -- left little finger stretched out to the left
Tab (not strictly a modifier key) -- varies, but most often left index finger
Left Control -- left little thinger, pushing down by the base of the finger (for me, this puts the tip of the finger just to the left of Caps Lock)
Left Windows and Left Alt -- varies, but most often left thumb.
Right Alt (known as Alt Gr on non-US keyboards), Right Windows key and Windows Menu key -- most often right thumb (though particularly for the menu key, this moves my right hand from the home position; since those are used relatively rarely, I don't consider that a real problem)
Right Control -- most often right little finger, putting the tip of the finger to the right of Enter
Right Shift -- most often right little finger
Backspace (also strictly speaking not a modifier key) -- most often right ring finger
(And I ended up having to actually specifically try most of these, because for the very most part I don't even consciously think about them, just like I don't consciously think about the positions of the alphanumeric keys; with few exceptions, the intended glyphs just magically appear on the screen as I press down keys on the keyboard.)
For the function keys (F1 through F12), I find that it's often beneficial to move your hands off the home position anyway, so tend to just reach for those with whatever finger happens to be conveniently nearby and that doesn't interfere with any modifier keys needed for the desired function. For the keys that aren't really a part of the alphanumeric set you pretty much have to move your hands anyway so I most often just settle for the finger that happens to "feel right" when the hand rests on the relevant part of the keyboard.
Now, this is for a straight ("non-ergonomic") keyboard; my own keyboard is a 105-key Unicomp Ultra Classic, which is basically the IBM Model M, which is about as without bells and whistles as they come and certainly, I am sure, does not count as "ergonomic" by modern standards (but I like the straight layout). These finger positions may or may not be applicable for other types of keyboards; for example, one of my coworkers has a Microsoft Natural Ergonomic Keyboard 4000 which frankly I simply cannot seem to come to terms with, but which he swears by.