Not to say whether they are a good idea or bad idea in general, but on thing worth considering is that publishing fees also act as a barrier to entry for less well-funded groups. Some journals even charge fees to submit (even if you are rejected in the end). This can be especially problematic for interdiscinplinary work -- in my field (applied math) grants are generally smaller, and if I submitting a paper to a biology journal that charges a submission fee up front is not always a triial decision.