Many (most) stem plants do this ... it helps them spread in a natural environment. And, no, I do not believe you can control this. The ones that do many, many roots (especially the big hairy roots!), are often called "weeds," and I personally find the roots unattractive as they multiply -- I've removed many of these plants from my tank over time. I know that if you keep some of these "weeds" pruned very low, they can look very nice and you do not see the roots.
For plants that send out occasional roots here or there, I often prune the roots off ... or, if they are not unattractive, I might leave them.
There are at least a few stem plants that seemingly do not do this at all -- like rotala wallichii, but that's the only one I know of, and perhaps I haven't had it long enough to see it do this.
Perhaps someone else will chime in, but other than pruning low, I have no answer for controlling visible roots.
I asked this same question a month or so ago here and Tom mentioned that it is completely normal. If it just gets aesthetically intolerable you can pull out the bottom and replant the tips. I got good results doing this with Rotala Rotundifolia, hygro, cabomba caroliniana, and Ludwigia Repens.