Radio waves need clearance around the direct line between antennas, not merely a thin visible sight line.
Why a visible path can still have a weak link: the Fresnel zone
Two antennas may see each other while a tree canopy, roof or ridge still reduces signal quality. The direct line is only part of the space used by radio propagation.
The first Fresnel zone
The first Fresnel zone is an ellipsoidal region around the straight path from transmitter to receiver. Waves taking nearby paths can combine constructively at the receiver. An obstruction inside this region can attenuate or diffract them even when it does not fully block the straight sight line. The zone is widest near the middle of the path; its size increases with distance and with wavelength.
A common planning approximation aims to keep a substantial part of the first zone clear, rather than assuming that optical visibility is enough. The precise clearance target depends on the link and terrain. At a field site, account for tree growth, roofs, land curvature, antenna height and the aircraft's changing altitude.
For intuition, the midpoint of a 1 km path at 5.8 GHz has a first-Fresnel-zone radius of roughly 3.6 m in a simple free-space calculation. The radius changes with frequency and geometry; a thin visual sight line is therefore not enough.
Field checks
Mark both antenna locations and their heights. Inspect the terrain profile, not only a map's straight distance. Note structures and vegetation near the midpoint. If signal changes sharply when an antenna is raised, partial Fresnel-zone obstruction may be involved, though interference or alignment should also be checked. Compare measurements at repeatable locations before drawing a conclusion.

The useful question is whether there is enough open space around the RF path at the actual frequency, height and range—not just whether the other antenna is visible.