Apparently they did have a bit of a spat a couple of years ago when everything was kicking off, but have since made up. Apparently they have a heck of a lot of respect for one anothers driving talent. Alonso's main beef was with the team, or in other words, with Ron Dennis, and now he's out of the picture everythings calmed down between them.
On a personal note, i've been very very critical of Alonso in these forums over the years. But, recently i've softened towards him, he seems to have matured a lot since he left Mclaren. Let's just hope he doesn't start throwing the toys outta the pram if/when Massa starts beating him in the Ferrari.