I think either way it was setting up to be a tough game. I think weather and travel is more likely to affect a west coast, warm weather team than Indy. The Chargers also had one extra game so far in the playoffs and the staff is less familiar with Belichick than the Colts' staff. So for those reasons, the Chargers would seem to be, on paper, a better match up than the Colts. On the other hand, I don't discount the role that emotions and bulletin board material can have in a game. I did not used to think such things could matter in a big game, but Belichick has convinced me otherwise. I think the Chargers -- much like the Patriots do -- have taken the perceived slights after last year's game and worked it up into a motivating rage. They would love to "disrespect" our logo this year.
So, in many respects, I do not see a significant difference and I'm not more comfortable with the Pats playing the Chargers than if it were the Colts.
All that said, I was still rooting for the Chargers against the Colts, simply due to the fact that if the Patriots lose the championship game, the implications of losing to the Chargers are not as bad as the implications of losing to the Colts. If the Colts had won the SB this year, along the way beating at home a team many thought was making a case for the greatest ever, I think they could have started to make a very compelling case to being close to the Patriots in the "recent dynasty" discussion. Two consecutive (and more recent) Super Bowls, two conference championships over the Pats head to head, and crazy numbers in the regular season for several straight years.
The prospect of a Chargers one-off super bowl win does not trouble me as much.
So, I was rooting for the Chargers solely in a disappointment-avoidance posture -- hopefully it won't turn into a careful-what-you-wish-for situation. If the Patriots lose the AFCCG, I'll be bitterly disappointed, of course. But it would hurt worse losing to the Colts, so in that sense I'm happy it's the Chargers.