I would. The more roots, the better IMO :)

Linda

Agree with Linda.

Dave

You could even remove healthy leaves and go deeper. If the seedling is tall enough you could lay the buried part in a trench and gently, I said GENTLY, bend the top upright. This exposes the roots to warmer soil.

tj

To add to tsufajunkie recommendation, you could lay the tomato on its side for a day or two and the top will naturally curve up then you can bury the stem up to the curve part.

The downside as implied by tsuga is the deeper you go the colder the soil is, which may be an issue in spring. Tomatoes don't like cold soil. Hence the horizontal planting recommendations.