Fusion, particularly as it's described in ST is very safe, pretty energy dense and gives you nice cheap fuel. The only real limitation appears to be size. You need a LOT of fusion generators to match the peak output of a warp core. (Sustained output for the E-D's fusion generators are probably about 240TW, which compares rather favorably for most estimates of its warp core output in the ~1100 TW/year for 3 years range)
(This will go into detail later but...) I wager that the main thing that requires m/am warp cores is crossing peak transitional thresholds for higher warp factors. Which means that the brief high peak output of an anti-matter reaction cores are more useful for ships that required going into higher warp realms like proper starships.
Everyone else (especially at lower tonnage) is probably happy with something that can sustain warp 6ish until the heat death of the universe, assuming you have enough deuterium.
Also in the episode "The Jem'hadar", it's actually interesting how well the runabouts held up in combat against the bug ships. The trio of DS9 runabouts seemed able to distract at least one of the bug ships. Ultimately it didn't save Odyssey
, but given the massive pounding the much much larger ship got, it's still impressive nonetheless that all 3 of them survived without any crippling damage. Which suggests relatively good protection, maneuverability and all around performance even if their overall output isn't all that impressive.