Memory Alpha explains that:
The transporter was capable of transporting multiple persons simultaneously. (DS9: "Vortex")
Which is pretty vague!
However, an important aspect to remember is that one of the defining features of the Danube class ship is their modular design as acknowledged in the DS9 Technical Manual.
In this spirit, I've found the following information (emphasis mine):
Standard Personnel: 1
Max Objects Per Cycle: 2
Supplemental transporters: Varies with Modules
There is also a two person transporter stationed in either the rear of the front cabin, or in the "Mid-Section" in-between the Cockpit and "Module" section. Aft of the front cabin are the mission specific modules. Based on the nature of the modular design, the runabout can be converted to other mission-specific requirements such as personnel transporter, cargo transporter, scientific expeditions, tactical assignments, prison transports, medical transports, etc. There is also an optional photon torpedo module on the top of the Danube-Class runabout.
Ordinarily it seems:
They are fitted with a two-person transporter and accommodation bunks for long missions
So, it seems to me that the Danube class' transporter capability varies depending on which module they have. The standard transporter only has the capacity for transporting two people at a time, as explained in the quote in the question. However, if certain modules were attached, it seems likely that the transporter capability was extended to transport more people at a time.