Yes, water stains do raise the wood grain much more than any other type stain, but to me it looks better, and that's why you have to: wet; raise the grain; dry; and 'dewhisker' a few time until the grain doesn't need dewhiskering again. Then apply the water based stain. Books from days past would have you put the stock in the sunlight to dry. Nowdays, just grab the wife's blowdrier and you can dry the wood rapidly.
One thing to mention about staining, is that some cheaper woods (and some expensive ones) tend to blotch when you stain them (that's when one area of the wood takes more stain than another, and you'll know it when you see it, and you can just resand it). That blotching isn't attractive and won't give you a pretty end result. If you're staining walnut, no problem, but I've found that if you have a really blotch prone stock of cheap wood, you can get good results in putting a coat or two of spray shellac (Home Depot sells it) on the stock, sand lightly, and then use a walnut colored wiping stain to actually paint grain on the stock. If you don't have the grain painted just like you like it, just wipe the stain off with mineral spirits before it dries and try again. After that has gone to your satisfaction, a couple more coats of shellac followed by a couple of coats of Minwax Satin Polyurethane varnish will look pretty good. I did that to a friends decrepit old 22 single shot stock and the walnut 'paint job' fooled them all. Sounds like a lot of work, and it was, but I had promised to refinish the stock and that's what it finally took to make it look anything other than godawful bad. Be careful when making promises.