Ok - think about how the body is meant to perform a rowing motion - like a rowboat or better yet a crew shell since this puppy is made for speed and setup most advantageously for each rower. They are pulling directly into themselves, meaning that they are perpendicular to the resistence (their torso for the most part is at 90 degrees to the plane of water which serves as the resistence). I will throw in the caveate that the torso is not stationary during the row and it is very much a full body pull but you do get the point. Your back's primary rowing power is directly back. This allows the lats to be most heavily activated throughout the range of motion.
Translating that motion into weights, the resistence for a weight is gravity which is on a vertical plane contrary to water's horizontal plane - both are the respective sources of resistence. Where the rower was upright at 90 degrees to the horizontal resistence, the weightlifter's resistence is now vertical - so 90 degrees to vertical means your back is horizontal to the floor.
So that's the essence of where the 90 degrees comes from.
Moving beyond that, rowing is a fairly fundemental motion and with significant weight it is hard to stay perfectly still and I'd venture a bit unnatural - you will find there are more dynamic methods of rowing with a barbell out there but this is the base (see the Johnsmith182 sticky at meso's training board linked here if you are curious - excellent read by the way - best 20 minutes you will spend: http://forum.mesomorphosis.com/showthread.php?t=12
). So anyway, you tend to pull back a bit with heavy weight anyway and that is how rows should be done heavy and explosive. You should be accelerating that bar into your body. So someone starting at 90 degrees generally ends up cheating back just a bit and that's okay.
In addition, a lot of guys lack the flexability to keep their back flat and perform the exercise as they get near the 90 degree point. In that case you shoot for 90 degrees but you go to where your body is comfortable.
The reason why I stress it is because we have all seen the dochebags in the gym standing almost vertical and rowing through a minute range of motion. This is . It doesn't allow for proper activation of the lats since you aren't pulling in but up, the range of motion is drastically reduced, and on top of that you wind up looking like a moron so there's really nothing good to come of it.
As for starting the motion at 45 degrees, I can't say it's optimal unless you can't get any lower (in which case flexability work or core strengthening would be my suggestion depending on the issue causing this). If you start at 45 degrees and row hard, you'll find yourself above 45 degrees at peak contraction and possibly significantly. Your range of motion is cut, your lats aren't getting proper activation because you are no longer pulling in but pulling up and you will end up relying on other muscles to generate the momentum (and that necessitates further straightening of the back).
So anyway, it's a soft rule when I say 90 degrees. I am fairly flexible and I can get close but not a full 90 (you see this in the goodmorning too - everyone has a different range of motion). That said, the soft rule is meant to provide the necessary margin to correctly perform the exercise. There is a hard rule right behind it saying that you absolutely must come as close as you are able to the 90 degrees. Significant deviation compromises the exercise.
Huge reply but it's better to give someone the full explanation. Give it some thought and do some rowing in the gym the next time - performing the motion makes it crystal clear. Be sure to work on accelerating the rep. A rower accelerates the oar through the water working harder and harder throughout the range of the stroke. He doesn't stop pulling hard once he gets the oar moving. This is critical to rowing success in the gym but watch your rib cage on the light ones.