Closed standards are usually better suited for their appliance, so having D3D was not an advantage, untill Glide hardware could not keep up due to delays at 3Dfx. Those delays where mostly caused by the Banshee project, that lead to the introduction of cheaper cards with 2D and 3Dfx. Even the Voodoo 3 (with V2 SLI performance and 2D) was part of that project. If resources would have remained on the VLSA100, that would have become the Voodoo 3 instead of the Voodoo 4 and 5, while leaving the sub $200 market to D3D and older 3Dfx generations. Sure, D3D cards have done well in the past years, but upgrading them was never as easy as with the 3Dfx accelerators, because Glide was almost 100% efficient in SLI and its bandwidth requirements where low enough to use PCI, even with VLSA100.
Adding to what T8000 said, it also had less incompatibility problems with the Glide games. If it was a glide game, it would run. Some didn't run on older Voodoo1 cards sometimes, but that was because it just didn't support something needed.
I can still remember playing Motorhead, in Glide it was a lot better IQ than Direct3D and ran twice as fast.