From what I've gathered if it says distance education or online on the transcript you will probably run into trouble. Online classes do have a stigma against them since a lot of them aren't through a brick-and-mortar university and are therefore easier than the traditional classes. Having said that though if you find a place that is either respected (ie. HES, Berkeley Online (maybe - their courses are at-your-own-pace sometimes), UNE) you should be fine. Also, if your "online" transcript doesn't actually say online (and it's not obvious that it was distance - ie. 3 states over) you should also be fine.
I took all of my prereqs in a traditional setting, but I have done many of my core classes online and am currently doing a computer programming certificate (plus the math/tech writing prereqs for a physics minor and microbio) online due to financial reasons. My transcript doesn't reflect the fact that it's online anywhere. I'm going through ccconline.org. They are CC credits, but the CC's in my state are well-respected, and there will be no way to distinguish the traditional class from the online class.
My experience with online classes is that they aren't any harder or easier, just different. For example, if your exams are online as well (the case for my classes - but some of the other schools do proctored exams) you will often get to use your course materials to take the exam. That means less study time spent memorizing stuff, but you need to still have a good idea of everything so that you can look something up easily and quickly. Conversely in a traditional class you will have to put in the time to memorize stuff in order to perform well on the exams, but you won't have as much busy work as the online class (weekly required discussions, homeworks, etc). In the end the time works out about the same but the focus is different.
I wouldn't recommend taking all of your prereqs online though. My school has all of them except organic (and they all have at-home lab components) but you still need the experience of taking traditional classes at a 4-year university to "prove" that you can do it (preferably a full-load).
Good luck!