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Depends on how you filter the tunnels.

If it's not filtered at all, a VPN IPsec tunnel sends all traffic through a properly established tunnel. It encrypts it and verifies both ends, but it will send a virus, trojan, worm, just as easily as it will good data. (It's sometimes described as a hard shell and soft inside security.)

You can filter the tunnel, (direct traffic to only addess x and port x), assuming you have the equipment and knowledge to do so.

But don't assume your VPN does this.

"If it's not filtered at all..."

Not quite that bad off. Our main network here is walled off from the tunnels. My main concern is clients infecting one another. I'm going to have to take another look at what's in place to prevent that (as opposed to playing on here more today) before I go home. Luckily, none of our VPN-connected clients have a large sales force that brings laptops in and out of their respective networks. The fact that I'm paranoid makes me not so worried about that happening (paranoia makes for good preparation), but it does make me re-check everything every time a new threat emerges.