It mostly boils down to this:
If you don’t have the resources to screen everybody and everything to the highest standards, which we don’t, you have to concentrate those resources intelligently where you think the risks are highest. This doesn’t mean that you perform no checks at all on the remainder - all hold luggage gets screened, all carry on bags are x-rayed, all tickets/passports are checked, etc. You can also allocate part of your resources to completely random enhanced investigations.
Depending on who you ask, about 2-3 billion people travel by air every year. Of these, how many are actually trying to blow up the aeroplane they’re travelling on? Ten? One hundred? I have no idea but even if it was 10,000 it is a vanishingly small part of the total. This is why profiling is essential.