A helium or hydrogen filled balloon could be used for transporting goods but there are many problems involved in doing so.
First, if hydrogen is used, there is a risk of the balloon catching fire and to prevent it would require the use of a special material to make the balloon.
Second, such balloons would be very large and special areas for their landing is required. Also, during flight, the large number of airplanes that fly today could easily strike a balloon.
And finally, the speed of these balloon is not very high compared to modern airplanes and though they can travel in a straight line between destinations, they will take a very long time.
I can think of a few other reasons why they haven't been put to use as you say they can, but the answer will get too long.