Of course they say that, because it's true, they would prefer it, but clearly because they allow you to take science classes at the CC it's really not that big of a deal - as long as you can prove yourself. Some schools don't let you take CC credit, so for them it is a big deal. But that doesn't mean that if your only fesible option for starting undergrad is to go to a CC and you take prereqs there that it's going to significantly hurt you. I took just about all of my pre-reqs at a CC, and then transferred and did well in my upper division classes, and got accepted to an Ivy League school, and the question of the validity of my CC pre-req's didn't even come up at the interview.
If you can start at a 4 year, thinking back on my experience and missing much of that "college" experience, I would say to take that opportunity. But there's nothing wrong with the CC as long as you can prove that you really are worth the grades that you earned there.