Most speakers don't have a clue what to do with the pointer. However it is an essential tool in an effective presentation.
A presentation is a visual and oral communication synergy. Slides should not stand on their own, or why are you up there talking? Your words are intended to amplify what is on the slide. A presentation is an attempt to achieve more powerful communication by combining the oral and visual.
The audience needs help relating the spoken words to the part of the slide that the words are explaining. If you are explaining the two axes of a graph, point to each axis as you explain it. If you are explaining 4 text bullet points, point to each item as you amplify its contents with your words. You need to help the audience connect the audio with the visual.
In general, a physical pointer is preferable to a laser pointer. The extension of your arm and the length of the pointer makes a physical line between your words and the part of the slide you want to discuss. A physical pointer is also easier to control and the speaker is unlikely to wave it around in a mindless set of circles.
Those presentations in a huge room with two widely separated screens can be a problem because a laser pointer only allows you to point at one screen at a time. Ask the tech people to close off one of the screens or at least tell the audience which screen they should look at.
Use the pointer with discipline! It is the key to connecting the audio and the visual.