The neighborhood around UPenn isn't that bad at all. Ten years agao it was a different story, but its starting to look more and more like Cambridge in Boston.
And...you can definitely find a room cheaper than $1000.00. If you look hard enough you can find some great deals in CC for between $600 and $800. A friend of mine just gave up an apartment between 18th and 19th on Pine Street (1 bedroom for $575.00).
Anyway, try looking on craigslist, Philadelphia Weekly Online, or City Paper. Look in these areas: University City, Art Museum Area, Graduate Hospital, Rittenhouse Square, and Olde City. These are all relatively close to where you'll be taking classes. There's also a lot to do in these neighborhoods as they're right in Center city. As far as looks go, Rittenhouse and Olde City are probably the nicest areas to live in. People tend to think that everything there is really expensive, but look and you'll find there are cheap places too. Graduate Hospital is up and coming. Its on the cusp of Rittenhouse Square and South West Philly. SW Philly is a tough neighborhood, but I know plenty of single women who live in Graduate Hosp area with no problem. The same can be said of University City. UPenn has a lot of money and they've put a s*** load of it into the neighborhood. The last thing they want is for Susie Ivy League's parents to pass them up and send their kinds to Cambridge because of the neighborhood.
Other neighborhoods to consider but that are farther away: Manayunk - (nice, clean, trendy, and increasingly expensive), Northern Liberties - (hipster kids, up-and-coming, lots of bars and venues springing up here), Queens Village/South Street area - (diverse, cheap and expensive, lots do around here).... I could on and on. Philly has a ton of neighborhoods!!!
Send me a message if you have any specific questions. I love Philly and would be glad to help out.