What is the difference between Ripple and Stellar? I went through the site but I don't see how Stellar differs from Ripple. I see that there are differences in distribution, everything is made open source from day one and the company is non profit instead of for profit as in Ripple. 

Both were co-founded by the same person and the technology seems to be the same.

What am I missing?
[Note: This answers the question as written and at the time it was written (and for quite some time afterwords). See a later answer for the current state.]

The Stellar code is a straight fork of Ripple with mostly trivial changes. It does have certain controversial features omitted (I assume on purpose) such as freezing. From a server and protocol perspective it has the exact same strengths (and weaknesses!) as Ripple does.

The client appears to have have had much functionality hidden/removed. For example it's currently impossible to set up trust lines.

The internal "currency" (transaction tokens) has been renamed from XRP (ripples) to STR (stellars). Sadly, "STR" doesn't even attempt to be ISO 4217 compatible.
The STR distribution model differs from the XRP distribution model including an "inflation" feature whereby new STR is issued (and for the foreseeable future, goes to the "Steller Development Foundation").