Yeah, the problem is that there have been court cases upon court cases, voter referendums, sales and aborted sales, and wild and crazy decisions from judges.
If you look at the link you provided, and click on a link on that page marked "Update", you will see that there is ongoing argument about who does own the land. Obviously the Association position is that they own it, however multiple judges seem to have ruled otherwise.
I can't see how the judge could think otherwise when it states, "The Mt. Soledad Memorial Association believes it has always owned the cross and holds the deed to the half acre parcel in question. The City of San Diego has not returned the money paid to it by the Association when the Association purchased the parcel in 1998."
What a mess.