You're right -- there is "good" and "bad" everywhere -- just like their are always opposing opinions to where you choose to live. No matter where you decide, there will most likely always be someone who has a different opinion. Just keep focused on what your goals are -- do you want a short commute? Do you want good schools? Do you want local shopping? What do YOU consider "good" and "bad"? If you stick to your own needs and what makes you -- and not others -- happy, then you should be ok.
Just remember to do your research on factual data -- like local crime rates, school ratings, etc -- and enlist the help of an agent who can help you find a home that meets all those criteria. Watch out for flood insurance requirements and HOA's, if you do stick with Natomas.
Overall, I have had several clients who have moved to Natomas, and they really like it. The proximity to downtown and the airport, the availability of retail, and the newer homes at a fair price, are what have attracted them to the community.
There are many communities throughtout Sacramento that can also fit the bill, though. So again, right down a list of your family goals, and start there first -- if you aren't finding exactly what you are looking for, maybe then you broaden your criteria.
All my best!