I poked around a little bit and this is what I found:
Taca Airlines will get you round trip to Guatemala City between $400 - $515 before taxes. Depending on your dates, you might get cheaper, but I just defaulted to the dates that auto filled.
I found this one day tour company to the ruins that includes an additional flight between $300 - $400 and starts in Guatamala City
http://www.tikalpark.com/tikgua.htm
You can fly from San Jose to Flores for a whole lot more (about $1150) and do it on your own.
I just changed the dates and I found CheapOAir that is offering a really cheap flight through the same airline for less than $400 when I put in dates for Nov instead of Oct.
http://www.cheapoair.com/Default.aspx?ta…
I looks like its going to be really expensive anyway you look at it. This isn't really that close to San Jose. You might be better off making a separate trip if you are on a budget.
In my research, I found this great 9 day tour of the Mayan Ruins all over Central America for around $900, if you decide to do it seperately at another time, this looks fantastic. Might have to do this one myself, lol.
http://www.latinamericacollection.com/pa…
Sorry I couldn't do better for you. The bus will definitely be the cheapest, but all your other options may be a bit expensive.