Birds eat the berries and excrete the seeds undamaged - squirrels will strip the aril from the outside of the seed and eat that,but they don't eat the seeds as such - they remain toxic.

also just because some things are toxic to us doesn't mean it is toxic to all animals. the converse is also true.

Many plants produce toxins/irritants to help hurry the seed through the gut so it doesn't get damaged in transit, when it leaves the body the seed is already in a dollop of fertilizer.
welcome to GoY too.

The flesh of yew arils is very sweet making them attractive to animals. I've tried tham and once spoke to someone who said he ate several hundred every year though he spat the seeds out.

As Bamboo said, the seed has a casing that stops it being digested. Over evolutionary time, the yews that didn't have a sufficiently robust seed cover died out as did the creatures whose stomach acid was strong enough to break down the seed.