Manny is illegitimate and Rodolfo and Maria's marriage was a shot gun wedding.
I was scrolling through some websites to find out more information about Maria because I found it rather curious that she went to college but didn't really have college job. At first I thought it was because she wanted to be a singer until I learned that her age at the time of the series was 30 and tgat would have made her eighteen when Manny was born. Also I noticed in the episode Adios Amigos that little to no people aside from the Titan were witnesses to Rodolfo and Maria's wedding and that they had Manny very quickly after.
So here's my theory when Rodolfo and Maria were dating they shall we say got a little too passionate in their relationship leading to unexpected pregnancy and Rodolfo being a hero and madly in love with her decided to do the honorable thing and marry her of course with a new baby on the way she had to drop out of college. So if this theory is true then I guess Rodolfo wasn't as "all good" as we thought he was. Wink, wink, nudge, nudge.