I read somewhere on this site that Kidney beans contains toxins so it is necessary to soak them. I soak them too overnight, but then I use the same water for cooking them. The water in question turns red after the beans are soaked. I do not throw away that water since it contains the taste, proteins, vitamins etc. of the beans. Haven't cooked beans yet with the fresh water, is the taste affected when cooked with fresh water. Am I doing wrong?
The toxin in kidney beans is destroyed by boiling for around ten minutes, which no doubt holds true for any toxin in the water as well. So there should be no problem with using the soaking water to cook the beans, provided you cook them properly.
It is sometimes suggested that one discard the soaking water in order to reduce flatulence.
This effect seems, however, to be based only on anecdotal evidence, and the efficacy of the practice is questionable. The problem is that flatulence is caused by digestion of fiber by gut flora. The majority of the fiber in the beans will still remain, and I would argue that the need for dietary fiber outweighs the gas-producing effect. I've also found that regular consumption of fiber is far more effective at mitigating the gas production than this type of trick.
By discarding the water you do remove both flavor and nutrients (as you suggested in your question). It's primarily a matter of personal preference, but I always choose to use the soaking water as a cooking medium.
My observation is that dry beans are packaged and shipped with a fair bit of their "natural surroundings" [read: DIRT and small ROCKS] in place. My preference is to rinse under running water and soak in fresh water and then exchange that water before cooking. I don't know specifically if it is "problematic" to not do this, but given the use of chemical and natural fertilizers, herbicides and pesticides it is comforting to at least "feel like" I have cleaned all of that off before cooking. My original equipment "Mark I Flavometer" (aka taste buds) says they come out better that way.