When fees are low, you could send the dust to a burner address (one at a time, each to a different address), or you could even consolidate the dust and your real inputs as long as the fees are lower than the dust is worth. Make sure to only use the dust input and your real input from one address at a time, so you don't link different addresses together (which would reduce your privacy).
yes, think of it as a bonus to pay for network fee on the next outgoing transaction 
546 satoshi input is enough to pay a transaction with 2-3 more inputs at 1s/VB fee rate
Consolidating that dust is a nice way to earn a few Satoshi from that attack, as pointed out by loycev.
unless you're getting annoying dust attack that will cost more to send than its own amount take a look at this guy spammed 1 satoshi to 750 addresses per transaction
https://btc.com/b6cba92e88dbdd0c5bf3305b881eede85b2168889c5fc8bf377918da3cf21e19
1SochiWwFFySPjQoi2biVftXn8NRPCSQC
1Enjoy1C4bYBr3tN4sMKxvvJDqG8NkdR4Z