I think they reject a higher percentage than 99%. It's probably closer to 99.9%, or even 99.95%. They get something like 1,000,000 applications per year. It's crazy.
I don't know why they say that: it's not impressive at all. Harvard has an application fee, Google doesn't. Anybody and everybody just submits a resume coz "it doesn't hurt".
GP: if they get 1,000,000 applications and 4500 people join: that's a 99.5% rejection rate even if you assume no one turns down the offer.