I live in L.A. (not Downtown, but close to Farmers Market). You are absolutely correct that when you do a point-to-point shuttle to Anaheim (or from Anaheim to L.A.), without stopping at the airport, it will be well over $100 (one way). I have used SuperShutttle for that in the past, although I had to call a specific "group desk" phone number to book the point to point because at that time their online system could not take point to point reservations. Anyway, I paid well over $100 for one way -- it was actually more like $120!
I then switched to another shuttle service called Sav-on Shuttle. They are small and lesser-known, of course, but I have had nothing but good experiences with them whenever I have used them (which has been several times in the last few years). They are always on time (early, in fact), and they are friendly and courteous. The price is still not cheap in any way, but it is a bit cheaper than SuperShuttle. Also, Sav-on Shuttle does not require a payment before your trip, as SuperShuttle does -- so it is easier to cancel and not have to worry about waiting to get your money back. Look up Sav-on Shuttle on Yelp and you will find mostly good reviews.
You might also want to look into Lansky (formerly DK's Livery, if I recall correctly) -- some folks speak highly of them, but I have never used them.