Does it have a bad effect on my career if I publish in Frontiers journals?
The short answer is, you shouldn't be too worried, but you should make some deliberate choices with your next submissions.
As @BryanKrause mentions, the quality of Frontiers in depends on the specific journal. Some have better editors than others, who will/are able to recruit better reviewers, and therefore a better review/editorial process. I have heard Frontiers in Neuroscience maintains higher standards.
Frontiers seems to revolve around 'special issues', so you will always need to considder who the specific editors of the issue are. I have noticed in some cases, these special issues are used to create an 'easy' venue for a specific community to generate papers out of a workshop or symposium. In other cases, the special issues can be considered quite serious.
Overall, Frontiers in, and the open-access publishing model in general, is very young. They are also trying out some rather radical ideas for the review process. Many people will be skeptical for a while, regardless of the quality. Some will embrace it, and also have a better opinion of others who embrace it. My expectation is that in the long term, Frontiers (or some other open-access journals) will win out, but this will take some time.
As a consequence, I'd say it is unfortunate if you published your best work in a Frontiers in which isn't of the best quality. But if you have other publications in more established venues, it is unlikely to count against you with a future hiring committee. My advice is to make sure your next paper or two are in very established journals, after which it is up to you if you want to push the open-access model more again.