Don't skimp on long distance bus rides. Budget "chicken buses" can be fun for a short ride, but for most the more comfortable first class buses are worth the price for long trips.
The route from Guatemala City via Poptun is served by three first class bus companies, Linea Dorada, Autobuses del Norte, and Fuente del Norte. The latter has for years run cheaper buses between Flores and Guate, but more recently it also runs day and night buses that include first class and deluxe seating. Downstairs "camitas" are plush, but especially from Guate at night, you had better have a light sweater to wear.
The route via Coban takes about 12 hours on buses, as opposed to the 8-10 or so via the other route, but it is more scenic. Plus, though you have to change buses in Coban, that is a destination in its own right. You would start out from Guate on Monja Blanca and switch to a minivan in Coban.