Mainly because it was a very fun game, and it advanced the first person shooter genre quite drastically. It had rooms above rooms, interactive objects, inventory system, in game dialogue, and plenty of weapons. Strife had some of the features, but the Build Engine expanded on it quite a bit. It was a huge technological advancement, and it was rather funny.
An inventory system was neither novel nor an advancement when it was employed in Duke Nukem 3D. Heretic, Hexen, and others had done it years earlier. Also note that the most popular FPSs to come after, the Quake series, Half Life, and Halo, do not employ a similar feature, because it breaks up the flow of play.