We get, on average, 200 questions a day. There are simply not enough active users to review, vote and comment on every single question.
This is an extremely high volume site:
If question askers don't take the time to read the help guide that's a risk they take. We simply can't personally tutor every new user who doesn't follow the rules. Trust me, I've tried.
Downvoting plays a very important role in the maintenance of the site. Filtering questions, invoking the question ban, and helping to detect spam (and get it deleted) are just a few of the important functions of voting.
tl;dr
While it is important to encourage users to add a comment when they downvote, it isn't going to happen every time. I don't consider this uninviting to new users, I jumped right in and never had a problem and I know scores of other users who did as well. If you take the time to write good questions, read the help guide and learn how the site works you won't have any trouble, and if you don't, that's why the voting system is here.
Ultimately, while the voting system may initially appear discouraging, it's actually here to make sure good questions get good answers, and it does it's job well.
Also, if you see a good question that has been voted down, vote it up! Good questions (and answers) should always be voted up.
Replies to comments:
If a community driven site can't be bothered encouraging new users and instead focuses on negativity, down-voting , for what ever reason, this place can never be seen as friendly/inviting/encouraging.
Actually for users that take time to read and understand the rules we are quite friendly inviting, and encouraging. It was so when I started, and I know of lots of users who started after me that will say the same thing.
If you can be bothered to down vote you can be bothered to comment.
That's only partially true. When I started downvoting I usually left a comment explaining why. However that slowly stopped so that now I only comment if it's not obvious why I'm downvoting. This is why:
We get about 200 questions a day. Let's say 50 of those are bad questions for whatever reason. Let's go on to say that I downvote and comment on 10 (which usually doesn't happen anyway). Repeat for 7 days. Now I have 70 downvotes and 70 comments.
That's a lot of time that could be better spent helping the user on their problem, if they would have only taken time to read the rules in the first place, not to mention 150 other questions that are more deserving of help (i.e. more on-topic, with askers who actually care, shown by the fact that they took time to form a good question).
Basically, if you won't take the time to write a good, on-topic question you can't expect us to always take the time to explain why you are downvoted, when the answer is right there if you would read it.