Why was the philosopher's stone in the snitch in Harry Potter?

Answer 1

The philosopher's stone was not hidden inside the Snitch, it was hidden in the Mirror of Erised and was later destroyed.

Nicolas Flamel and Albus Dumbledore were protecting the philosopher's stone because they knew Lord Voldemort was attempting to steal it. Dumbledore modified the mirror so that only somebody who wanted the stone, but not to use it could get it. That meant Voldemort could never have gotten it out.

The resurrection stone was hidden inside the Snitch. Dumbledore did this because he had to find a way of getting it to Harry that couldn't be intercepted by the Ministry of Magic but that also wouldn't throw him off his journey.

Harry could only open the snitch when he told it he was about to die, something Dumbledore intended him to discover when all the Horcruxes except the one inside him, had been destroyed. This was to allow Harry a moment with those he loved before he died. Giving him access to the Stone beforehand may have resulted in him becoming obsessed with spending time with his lost ones rather than trying to save himself and everybody else.

Answer 2

No, the stone was in the Mirror of Erised.