I also have Midwest (Iowa) experience and yes, the traffic to and from Fremont can be nutso. And they get traffic going both directions during both the evening and the morning commutes, since there's people going up to SF and down to San Jose/Silicon Valley to work.
Another place to check out to live would be San Leandro. There are plenty of safe areas left there and it'd be closer to SF and Oakland. There's some interesting older neigborhoods there with some character. And a really cool old diner/greasy spoon called The Fifth Wheel. You might be able to get a place in SL with a yard and it would be waaaay cheaper than Fremont, which is getting very expensive, due to its proximity to San Jose. I don't know how it's possible, but according to an article I read last week, SJ now has a median home cost even higher than SF.
And despite what Aya says, do not completely discount East Oakland. It's probably the cheapest part of Oakland for rentals now. And parts of it really aren't that scary. In East Oakland, some GENERAL guidelines are: Above 580 is better than below. Or at least, above Mac Arthur. If you're near International Blvd/E.14th St below (west) is better than above. Avoid anything near Bancroft. Check out the Eastlake and San Antonio areas, which are near Int'l Blvd from about 1st Ave to around 25th Ave. Not too bad. There are some pretty okay neighborhoods in the Laurel District, which is centered around Mac Arthur @ 35th Ave. The Dimond District, near where I live, isn't too bad, either (Mac Arthur @ Fruitvale Ave.) And there are some okay places near Mills College and off upper Seminary and High Street. Plus, there are some "hidden" neighborhoods in deep East Oakland with addressess that make them seem like they should be totally dangerous, but somehow they're really nice. And there are a lot of places down there with yards. You just have to look. Drive through the neighborhood. If there are a lot of people hanging out on the corners doing nothing at all hours, a lot of bars on the window, a lot of gang graffiti, and more liquor stores than trees, it's probably not too safe. If you see a lot of families and well-kept houses, the crime probably isn't too bad.