I was wondering if anyone could tell me how to get from San Pedro Sula to Flores by bus. I read there are only several border crossing points for getting from Honduras to Guatemala. Would it be best to go from SPS to Puerto Barrios, and find a bus from there to Flores? Or is there anything direct? Any advice would be much appreciated, thanks.
It's 6 of one and half a dozen of the other whether you go from San Pedro Sula toward Copán and the border at El Florido or toward Puerto Cortes-el Corinto border crossing-Puerto Barrios where you would then catch a Flores bus.
Haven't done the 2nd one. Copán and the ruins there are definitely worth a visit if you've never seen them; a whole different perspective as this sect were the artisans with intricate details compared to the grand temples of Flores/Tikal.
From Copán it's a quick ride to the border, transfer to the público for Chiquimula, and catch a Flores-bound bus. I did this taking the first border truck of the day out of Copán at 6am and was in Río Dulce shortly before noon - about the half-way point on up to Flores.

There is an express bus that operates between San Pedro Sula and Belize City.
It departs from San Pedro Sula on Tuesdays from the Belize Embassy in Honduras, and goes through Flores on its way to Belize City.
Cost: US$60.00 one way.
This schedule was last updated in April, so you should contact Mundo Maya Travel to confirm:
Phone: (501) 223 0457 / 223 1235.
Email: mundomayatravels@yahoo.com
The water taxi route might be a bit longer.
See bus & water taxi details here: http://belizebus.wordpress.com/

I know this is old, but I just did this trip and thought I would post for future reference.
There is a bus you can take that leaves at 5:30am that leaves from the San Pedro Sula Bus terminal called the Fuentes De Norte. Also called Maya Del Oro. (same bus) They will tak you from San Pedro through the Coriento boarder crossing with Guatemala and has a direct bus from Morales (where you switch buses at a gas station) to Santa Elena/Flores/and Tikal. If going to tikal remember the last buses leave Flores/ Santa Elena at 2pm.
It was realively easy and inexpensive! Hope this helps people making the same trip.