I think the problem is that we're making animals, which have adapted through natural selection, go extinct. Those other 99.9% of animals were most likely ones that did not evolve or move after changes in their environment, and paid the ultimate price.
It's not about what the animals do for us (i.e. as a food source), it's about what role they play in their own ecosystem.
For example:
Pretend that the major predator in an area goes extinct due to poaching, or an even more common problem; overfishing.
Then, the populations of primary consumers/secondary consumers that were it's prey will increase greatly over the next generations until they begin to deplete their own food sources (producers).
It throws the whole ecosystem out of balance, and the ecosystem may not be able to recover.
Now, obviously that was a worst case scenario, but then we really can't tell which extinctions will cause the most damage, so it's ideal to stop all unnatural extinctions.
And also, it gets to be a problem when you're having more extinctions than the normal background extinction rate.
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“Earth provides enough to satisfy every man's need, but not every man's greed."
-Gandhi
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