Senators can't and don't vote every single time on every single issue. Rubio is campaigning for President which is extremely time demanding. Now, if he's missing vote 'cause he just doesn't wanna be present, and, isn't working on his campaign trail then that's bad. For the record, Trump actually put Rubio on blast FIRST right here:

http://www.politifact.com/truth-o-meter/statements/2015/sep/17/donald-trump/trump-says-marco-rubio-has-worst-voting-record-the/

Also, Rubio may have made a mistake with his assessment of Obama's missed votes. The following information is taken directly from congress. Scroll down to 'Voting Record.'

https://www.govtrack.us/congress/members/barack_obama/400629