Realistically, a solar flare is just a minor radiation hazard, since it's mostly alpha particles that can't penetrate skin or paper, let alone tinfoil. It's dangerous to someone without a spacesuit, but even then it won't be instantly lethal... far from it, I believe. Black holes will obviously annihilate anything that enters them, unless it uses FTL and powerful gravity manipulation to escape.
Realism isn't always interesting, so other effects might occur. After all, sometimes tornadoes take you to Oz, so why not have solar flares scramble electronics or cause hallucinations, or have black holes send you to Kansas or cause you to become trapped in a reality TV show unless you can outwit the evil alien host?
I answered this thread before in a chat, but not here: If a ship can survive atmospheric reentry, it can survive anything an Earthlike planet could throw at it (except maybe being directly over a super-volcano eruption, but that's unlikely.) To find really threatening weather, try Jovian planets, or planets with corrosive atmospheres and unearthly powerful storms. Stars will wreck you too, if you fly in one.