There are actually quite a number of tools that can be used to passivate a structure. They all work differently, and none are perfect at what they do. If you're dealing with organic molecules, these codes will work far better than if you're dealing with inorganic complexes.
Here is a list of some tools you may be interested in:
PyMOL has an H Add function. PyMOL accepts many kinds of formats.
Olex has a similar command as PyMOL called
hadd, as described here. This program is widely used when dealing with CIFs.Reduce, Chimera, and MOPAC can all be used to automatically add H atoms to PDB structures.
CrystalMaker has an option for automatically adding H atoms in its Molecule Builder utility, as listed here.
Avogadro has an option for automatically adding H atoms to a structure, as described here.
Materials Studio has an option for automatically adding H atoms.
There are likely many, many others.