As with many things, it depends on how it's done. If there's no disclosure and editorial keeps referring to certain products or companies without any implication of a relationship, that's just payola. Sadly, there are plenty of outlets and magazines that are suspected of or have been caught doing this.
Increasingly, though, reputable media organizations are doing collaborations with brands, such as with merchandise, pull outs, giveaways, or in clearly marked 'products we like' sections (essentially advertising as content - super popular in fashion and women's magazines). It's a rapidly spreading model in the magazine space in particular. Monocle magazine is one of the exemplary examples - http://www.reallypractical.com/2009/07/06/is-monocle-the-fut...
The big traffic/small CPM model is still too lucrative online for the bigger online publishers to spend too much time on the newer ideas, but the hands of other media have been forced by tumbling revenues and, in a funny twist, are becoming more progressive.
On quality, though, the readership will ultimately vote with their feet (or clicks) - outlets that fall into the payola trap will suffer audience drops and legal trouble, outlets that transparently entertain or inform their readership in conjunction with advertisers will thrive (as Monocle is).
Separate from pairing up with media outlets, many advertisers are now going 'direct' to audiences with content-driven campaigns (not just videos, but entire content sites). Digitally prodigious companies and startups have been doing this for ages with blogs and the like, but the approach is now becoming mainstream and being taken on by the big brands.
Ad blockers are next to useless on all of this but, IMHO, the end result is better. Outlets and brands have to start telling interesting stories and sharing interesting content, instead of tricking us into clicking graphics and becoming leads.