Because of the economy of scale. As an example, if I buy a book from Amazon at $25 then GST is just $2.50
There is more than one person and several departments/agencies/companies involved in processing my GST transaction, but for simplicity lets assume it's just one person and leave out all the overheads of employing that person or overtime rates etc.
Assume, albeit generously, that processing time to process my parcel including identify the contents, calculate, gather and remit that money through the accounts system would be 15 minutes. After we are government workers...
If somone is being paid around $48k per annum (Based on ABS average aussie weekly earning stats) that equates to roughly $33 an hour, or around $8.25 salary for the 15 minutes work.
So, by my (very rough) reckoning it would cost the government an additional $5.75 for me to buy a book from Amazon if they charged GST. And my purchase is one of thousands of extra parcels to process every day.