...are you kidding me?
Dude, cross-ups are very, very effective. Aside from raising damage for a combo, they assist you with pressure tactics and also guaranteeing you a combo if you manage to jump over a projectile and get within a range close enough to reach them. If you try to block the cross-up, you're usually caught in offensive pressure and will be struggling to get out.
A logical route to take would be to try to jump away, as you'd take less damage from one jump-punch rather than standing there blocking...but with some characters you could get caught in an anti-air combo if they're smart, like say Kitana for example. Cross-ups have become a universal and effective tactic in this game.
But you are right to say that they are very unsafe and punishable if they become predictable. However, don't expect a smart player to be predictable with it. As Sao told me, the big names have kept a limit to their cross-ups and jumping because there are many counter tactics for those who like to stay in the air. To provide a list, you might be able to jump-kick them, hit them with a projectile, use an armored move (like Rain's Enhanced Super Kick), or combo the shit out of them if you bait out a jump-in punch and get it to whiff.
All the same, don't underestimate them. It takes a lot of patience and skill to be able to anticipate jump-in punches...otherwise they're a deadly threat.
