Well, a line is defined between two points, so I don't think a single dot can be created. You can create a very small circle if you only want one dot.
If you want to have multiple dots in different places, then with the

tool, simply click where the dots should be and make a line.
Then, with the line selected, go to Object -> Fill and Stroke (Ctrl + Shift + F)
Go to the 'Stroke style' tab, and you'll see drop-down-list options with the title 'Start Markers', 'Mid Markers' & 'End Markers'
Search for an appropriate marker (for example dotM) and set each of the three options to that marker. This will make every point that you clicked on to be replaced with the marker. To increase/decrease the size of the dot, play around with the stroke width.
Now, to get rid of the ugly line, go to the 'Stroke point' tab, and hit the big "X" to disable the stroke.
The above method can even work if you only want one dot (make a line between two points, set the start marker to a dot, and then disable stroke)