Yeah, that is a pretty huge con. A little reading up (google searching) revealed a common opinion that most people don't take online degrees seriously, unless they came from a college or university that has a fairly well-known brick-and-mortar presence. Also, regional accreditation seems to be "generally" preferred over national accreditation, so I'd guess the safest bet, if I had to do it online, would be a regionally accredited school with a large physical campus with an online program.
example posts I read:
Get an Online Degree Employers Take Seriously
Are online degrees taken seriously?? | San Francisco | Yelp
Do you think that employers take applicants with "online" degrees as seriously as those with traditional ones? - Yahoo! Answers
The credibility problem with online degrees seems to be pretty big, but I got the impression from those posts that people are coming around, and I could only imagine that will get better (ie online courses will be taken more seriously in the future). Still, it sounds like a "gamble" right now.