] is a graphics directive which specifies that points which follow are to be shown if possible as circular regions with diameter d. The diameter d is given as a fraction of the total width of the graph.
PointSize can be used in both two- and three-dimensional graphics.
The initial default is PointSize[0.008] for two-dimensional graphics, and PointSize[0.01] for three-dimensional graphics.
See the Mathematica book: Section 2.9.3.
See also: AbsolutePointSize, Thickness.
The point on the x-axis is more visible in the second plot.
Evaluate the cells to compare the graphics.