Publications like this (http://lazyfoo.net/tutorials/SDL/09_the_viewport/index.php) say that the viewport causes rendering to occur to a portion of the window while still having the same coordinate system (particularly, size) as the window.

Maybe it works with the texture they're using as an example (and I haven't confirmed that it does), but it does not work when filling rectangles, say.

For example, without a viewport, I draw this: http://i58.tinypic.com/28ibuw3.png
Then I set a viewport 2/3rds of the window and draw the same thing.
I expect to see the same image scaled down to 2/3rds of the window, as in the article above. Instead, I see this: http://i61.tinypic.com/35lx2f8.png  It is clipped, not scaled. In fact, setting the clip rect gives me the same output. Because it would be pointless to have two rectangles with the same behavior, I assume that is a bug.

Here is a sample program to reproduce the behavior on my system:

#define SDL_MAIN_HANDLED
#include <SDL.h>
#include <stdio.h>

void FillRect(SDL_Renderer *pRenderer, int x, int y, int width, int height, Uint8 r, Uint8 g, Uint8 b)
{
  SDL_Rect rect;
  rect.x = x, rect.y = y, rect.w = width, rect.h = height;
  SDL_SetRenderDrawColor(pRenderer, r, g, b, 255);
  SDL_RenderFillRect(pRenderer, &rect);
}

int main()
{
  const int Width = 400, Height = 300;
  SDL_Init(SDL_INIT_EVENTS|SDL_INIT_VIDEO);
  SDL_Window *pWindow = SDL_CreateWindow("Window", 100, 100, Width, Height, 0);
  SDL_Renderer *pRenderer = SDL_CreateRenderer(pWindow, -1, SDL_RENDERER_SOFTWARE);

  SDL_Rect rect;
  rect.x = 0, rect.y = 0, rect.w = Width*2/3, rect.h = Height*2/3;
  SDL_RenderSetViewport(pRenderer, &rect);

  while(true)
  {
    SDL_Event e;
    SDL_WaitEvent(&e);
    if(e.type == SDL_WINDOWEVENT && e.window.event == SDL_WINDOWEVENT_EXPOSED)
    {
      FillRect(pRenderer, 0, 0, Width/2, Height/2, 255, 255, 255);
      FillRect(pRenderer, Width/2, 0, Width/2, Height/2, 255, 0, 0);
      FillRect(pRenderer, 0, Height/2, Width/2, Height/2, 0, 255, 0);
      FillRect(pRenderer, Width/2, Height/2, Width/2, Height/2, 0, 0, 255);
      SDL_RenderPresent(pRenderer);
    }
    else if(e.type == SDL_QUIT) break;
  }

  SDL_DestroyRenderer(pRenderer);
  SDL_DestroyWindow(pWindow);
  SDL_Quit();
  return 0;
}

It also reproduces without SDL_RENDERER_SOFTWARE for me.