Leaving kind and instructional comments, especially for new users, is a great way to create a welcoming community.
However, rate-limiting downvotes doesn't seem like it'd do much to assuage a new user who has posted a less-than acceptable question. I've seen plenty of examples of users completely freaking out on Meta over a single downvote (even on posts that have received several upvotes), so I don't think that receiving two downvotes is that much more painful than receiving one.
Once a post has received 3 downvotes, it's removed from the main page, which sort of limits the damage already. You don't have bad posts hanging around attracting more downvotes... they are automatically hidden.
However, the ability of the community to swiftly and decisively respond to spam and abusive content would be greatly hindered by rate-limiting downvotes. Getting content off the home page is exactly what spammers don't want you to do, and every extra minute that their content is seen by users is money in their pocket and incentive to post more.
So, rate-limiting would have relatively little benefit but could do a lot of damage to the community. The best solution is: be nice, and leave a comment.
For context, here's a query of all (not-yet-deleted) questions with a score of less than -3 posted by a user with less than 10 rep and where the question has 0 comments. There aren't that many... currently 2. Note that this is not live data... there's a data dump (monthly, I think) and many questions end up deleted before that data gets dumped. Perhaps someone with access to live data (and who can see deleted questions) would like to elaborate, but I'm not convinced this is a rampant issue.