Of the three variables that control exposure, ISO is the one with the least creative effect. Aperture directly influences the depth of field. Shutter speed controls the amount of motion blur. ISO on the other hand "just" generates noise if too high.
So giving your camera automatic control over ISO doesn't limit your creativity, and helps you focus on more important settings. The advice "don't use auto-ISO" usually is due to the fact that in low light situations, the camera might choose a ridiculously high ISO values (causing excessive noise) to make up for possibly poor speed and aperture choices without you noticing it.
In my opinion, there are better tools than disabling auto-ISO completely to prevent excessive noise. As other answers already state, you can set an upper limit for auto-ISO on most cameras. This means you can set a maximum allowed level of noise, but you camera is able to match ISO automatically if you specified your preferences on speed and aperture. There is no harm in using a lower ISO than the "maximum acceptable noise level ISO" you specified.
Another way to handle ISO setting offered by most cameras is not setting a hard limit on ISO, but just display a warning if noise will be high. This allows you to get a one-click choice in low-light situations: When you half-push the shutter button, you get a warning that the picture will be noisy due to high ISO. You can decide in that second whether you continue with the shot and tolerate the noise, or you think "oops, I forgot that I chose 1/1000 shutter speed for the outside shot 10 minutes ago, let me fix that".
Or, on a higher level: If you shoot "P" anyways and let the camera guess appropriate settings, turn on auto-ISO to give the camera more freedom to choose an appropriate point on the exposure triangle. Choosing P is a strong indicator that your preference is clearly on "getting a shot done", not on fine control over the exposure details. On the other hand, if you shoot primarily M, you might want to lock in or limit ISO too, to get full control over the exposure yourself. There are basically two ways to use M, I consider both valid: Either you choose ISO by hand, which will yield a user-defined exposure without any camera heuristics interfering with you, or you use auto-ISO to have the camera pick a adequate ISO for "correct" exposure. In the latter case, use the exposure compensation setting to adjust exposure in case the camera over- or underexposes the image compared to your expectations or requirements.