Perhaps a good way to monetise without alienating their core users would be to only advertise on the default subs. The vast majority of users are there, including the less technical users who might be more likely to actually consume the ads instead of ignoring or blocking them.

Another idea which I saw the Whirlpool forums do in Australia is to only advertise to those who aren't logged in.

If the sub-communities continue to thrive I can't see Reddit fade into obscurity any time soon.