Exactly as Double AA and Monica Cellio point out in the comments — the article is talking about Torah scrolls, i.e. the text of the Torah written on parchment according to specific rules, rolled around wooden 'atzei hayyim, to be used during ritual readings of the Torah in synagogue. We do have older books containing the text of the Torah, or even the TaNaKh, and of course the Dead Sea Scrolls represent a very ancient tradition for almost the entire TaNaKh. The article itself explains:
The find isn't the oldest Torah text in the world. The Leningrad and the Aleppo bibles - both of them Hebrew codexes, or books - pre-date the Bologna scroll by more than 200 years. But this is the oldest Torah scroll [according to the professor].
There are many reasons why Torah scrolls haven't survived... Many were no doubt destroyed in the various times when Jewish communities were being persecuted. And in any case parchment texts will decay and wear out with age and regular use. Since it is common practice to bury a ripped or worn out Torah scroll, it is rare for scrolls to be preserved for more than a few hundred years. This one is certainly a marvelous find!