It is not a virus. Windows SmartScreen filters out new, unknown software. For some reason, someone probably reported it to Google as a virus rather than tell me. I've updated the download to be on GitHub. instead. If Windows Defender tells you not to run it, click "More info", then "Run Anyway". I've published the source code now, too:
github.com/Miclebrick/Schematic2Json/

Hello all. I've made a new simple utility that converts a schematic file
to a .json mesh file. For most users, you simply have to extract the
zip folder somewhere and run "Schematic2Json.exe". Then, you enter the
location of your schematic file and it will create a json model from it
in the same folder as the schematic. If you want to run it from a script
or something, you can just supply the path in the first command
argument, and put "nopause" in the second, so it doesn't pause after the
operation is complete. Example: "schematic2json
"<pathtoschematic>" nopause"

For the textures, it uses the white wool texture by default. The UV is randomly picked. If you build with wool or stained clay, it will use the wool texture of the same color as the color of the block you used. It randomly picks which pixel of the texture to use for each voxel, but you may disable this with the "nonoise" parameter.

Command line parameters:
To use command line parameters, you need to run it as a command like this in your command prompt:
schematic2json "modelschematicfile.schematic" nonoise nopause
This converts modelschematicfile.schematic to modelschematicfile.json, and since it has the parameter "nonoise" and "nopause", it will not randomly select pixels and it will close immediately after finishing.

List of parameters:
nopause - Closes right after completion
nonoise - Disables random pixel selection

Mac users:
You'll have to use Mono to run the application, as it is written in C#.
http://www.mono-project.com/download/ to get mono.
After installing mono, run "mono Schematic2Json.exe"

Libraries used:

- JSON.NET json.net
- fNbt github.com/fragmer/fNbt

If you have any suggestions, want to make a comment on something, or need any help please ask/tell me in the comments!