I don't think that is what he's getting at... I assume he's already got
both installed and is worried if Windows gets a virus can it hurt his
Ubuntu installed, the answer is maybe.

If malicious software gets in and changes your MBR (master boot record)
then it can overwrite the partition table and while your data will still
be there your computer won't know where what partition and you'll be
unable to access it. I don't think many, if any, currently active
viruses actually do this, but it is possible.

Assuming you run Ubuntu most of the time, my advice is setup a cron
script to use dd to copy your mbr containing your boot sector and your
partition table to an off-disk location, a floppy (ew) or an SD card or
just upload it via FTP off-site, it'll only be 512 bytes so very easy to
upload.

Then in the event anything goes wrong you can boot from the live CD and
retrieve the file from wherever it is you put it and restore it using dd
again.

Doing this is part of my full backup solution and has come in handy not
for viruses but there was a Windows update that rewrote the MBR to
Windows liking and made Ubuntu disappear, I just did what I outlined
above and presto, it was back.

Oh, also, be aware that individual files should be safe as long as
Windows can't read them, so if you use ext2 or 3, hfs, reiserfs, etc...
Windows can't natively mount these file systems so a virus getting into
the system would have to install a specialized driver into Windows to
allow it to read them before it could specifically attack files on those
partitions.