Unless a creature's lowered its spell resistance prior to being rendered unconscious, a healing spell's caster checks that creature's spell resistance
According to the rules, a spell noted as harmless in its Saving Throw entry does not automatically overcome spell resistance. Further, a creature that's unconscious does not automatically lower its spell resistance.
A typical creature must take a standard action to lower its spell resistance (Player's Handbook 141 and here). No description of spell resistance (PH 177 and here, Dungeon Master's Guide 298–9 and here, Monster Manual 315 and here) says that a creature automatically and without taking an action lowers its spell resistance against spells labeled as harmless or when the creature loses consciousness. (It is a point of some contention whether or not spell resistance (and other usually continually active special abilities) end or are removed when a creature dies, though. Ask the DM.)
Even when the DMG says, "A creature’s spell resistance never interferes with its own spells, items, or abilities" (298 and emphasis mine), it does not follow that up with anything resembling what happened in the session that the question describes.
According to the rules, the caster of the cure serious wounds spell should have checked your PC's spell resistance, and, if the caster failed to overcome your spell resistance the cure spell should've failed.
What you may want to do
I suggest raising this issue privately with the DM. Explain that while you're happy that your PC's alive, according to the rules SR doesn't work the way that it was played during that session. It's possible that the DM will institute the way it was played as a house rule. While this DM has never experimented with such a house rule—I've never tried a house rule like Harmless spells overcome SR automatically, and unconscious creatures automatically lower their SR, for instance—, this seems a reasonable house rule in the abstract, especially as a modification to an ability that the game, in my opinion, tends to overvalue in its current form, especially when it's in the hands of a PC. Such a house rule, though, will cut both ways.
For example, a drow priestess can now heal a drow comrade who lacked the foresight to lower his SR before she cast cure serious wounds… without the risk that her efforts will go to waste. On the other hand, the drow priestess's flame strike spell will also automatically overcome the SR of her unconscious comrades caught in the spell's cylinder. So it goes.
However, what this DM would do were this brought to his attention is explain to the players how he made a mistake and that from now on we'd play by the rules. The Dungeons & Dragons 3.5 rules are clumsy, particular, scattered, and fill multiple bookshelves. No DM can be expected to know them all, and mistakes will be made.