The only way to do this from the UX only is to turn off the plotting of trailing zeros (suggested by @Anurag0911). However, this does not help you with any other zero values.
Expanding a bit on the suggestion by @ankit_cheeni to filter out zeros from the chart, you can actually "trick" Anaplan to avoid plotting a zero value by replacing your 0's with NaN's. While you can't manually enter NaN into a line item, you can write a formula that will return NaN. I suggest adding a NaN value to a System constants module so you can use it across your model as needed.