First advice ... don't take the shuttle vans! You'll feel totally ripped off!!
But, you can start taking vans and buses telling them you're going to Flores ... so they will make your conexions much faster.
Anyway, this is the route you'll mostly have to follow. From Coban to Raxruja (Q$ 20) ... it's faster if you avoid goinig all the way to Raxruja and you ask to get off at the intersection in San Antonio Las Cuevas. You'll end up at a gas station where you keep going to Sayaxche (another Q$ 20). This van will drop you off at some river shore where you can take a small motor boat (Q$ 2) to cross it. You'll see more vans in the other side, those will take you to Santa Elena (Q$ 15)... which is linked to Flores through a bridge.
Flores is walking distance from Santa Elena, but if you have lot of baggage... you can take a small motor-cycled taxi for Q$ 5.
There are some minibuses departing a few block north/north-east of the Parque Central ... the tickets cost Q$ 25.
I can remember exactly where the bus company is, but if you ask around... people know it, it's a small town.
I wanted to see not only the ruins of the Peten, most notably Tikal and El Ciebal, but also the Mayan culture of the upper highlands, where Coban, Uspantan, and Lago de Atitlan are located. However, I didn't want to take the route that led through Guatemala City and the touristy, albeit pleasant, Antigua. At the time Lonely Planet and other guide books described the mountain roads as unpaved, long, and dangerous. However, at Flores we inquired at the van stop about going to Coban and found this route good. Other VT members have followed my advice. This road leads from Flores through to Sayaxche (the closet pueblo to El Ciebal ruins, among others), where the road stops at El Rio Passion. At Sayaxche passengers must transfer to river ferry and then catch another van for Coban in Sayaxche. The route through the mountains passes through villages and crossroads, and there is a possible path to natural wonders at Lanquín. We tried going Lanquín but no van went there, so we retraced our path a bit and took a van direct to Coban. I recommend a stop in Sayaxche. The van driver's assistant will strap your pack or luggage to the roof with all the cargo, and you will not lose a thing. The service is excellent, and the drive through the mountains a thrill.
A recycled American school bus makes a daily run between Coban and Uspantan, the Mayan Highland homeland of Nobel Laureate Rigaberta Menchu. One can wait in the main plaza in the afternoon and ask around for the right bus, or wait uptown at the Coban street stop shown in the photo below. This bus ride climbs several thousand feet along a mostly gravel road, crossing on turns streams that flow over the road without aide of a culvert. Laden as our bus was, with not even standing room for the conductor and more than a full load on top, I worried with each such creek whether the weight of the bus might break an axle in the mud, creating an avalanche down the cliff. This is not a bus ride for the faint of heart, but it was one of the greatest transportation adventures I've ever had. I didn't mind standing the full three hours. The price of the bus is paid to the driver or conductor, and for all practical purposes luggage is well tended by the conductor. The only other tourists on our bus, a couple from Europe, insisted upon bringing their backpacks aboard rather than have them hoisted on top, but this was certainly an inconvenience for other passengers. At Uspantan, my wife left her purse, but I ran uphill fast enough to catch the bus. The driver searched with great concern, and smiled when he found it.
I went to Coban from Sayaxche by public minibus. It was cheap ($6 for 5 hours of travel). The bus stopped often, like a city bus. At the Chisec stop, children surrounded the bus offering sandwiches and drinks. Most of the time, the bus was (over)crowded, but it was picturesque and the views were grandiose. Even when packed like sardines, the travelers were respectful of one another and good humored.
From Coban to Antigua, I took a tourist shuttle instead. More expensive of course, although reasonable ($25 for 5 hours again). Not crowded at all, but listening to the brainless babble from other tourists made the time seem long - not to mention the depressing scenery toward the end (around Guatemala City).
My guidebook writes: “the road east of Sacapulas is one of the most beautiful, and roughest mountain roads in all Guatemala, with magnificent scenery in the narrow valleys. Truck to Cobán … seven hours, if lucky, usually much longer”. (Footprint; Mexico and Central America 2000).
Even though I had read this, I still went on this road. We considered to take another route, but it would be a detour, and we didn’t mind a rough trip. -------------------------------------------------------------------------------------------------------------------------------
We started out from Nebaj, by catching the bus to Sacapulas (1½ hour). It was full so we had to stand up most of the way. Then after waiting ½ hour, we got on a bus to Aspantan, this trip took 2 hours. After lunch here, we got a lift with a pickup to the next village, and after walking to the edge of this village, we got a lift with a truck, that drove all the way to Cobán (4 hours).
The whole trip took very long time and it was late as we arrived to Cobán. We were tired, hungry and dirty. Since the road all the way had been dirt road, it was a very dusty trip, especially the last long part, where we sat back in an open truck. The truck that took us up, where owned by a family and they were heading home after visiting some relatives. Some of their kids also sat in the back with us. We also picked up other people along the way. This way the family earned some money for the gas (we paid around 10 quetzales for the trip with this truck).
The roads were very poor, and at some point we drove 30 kilometers in two hours! Looking at a map, it only looks like the route is 100 kilometers long, but it takes very long time, but I think it is worth it, as one really get to see beautiful landscape and meet the locals.