People take CJ/SJ because most of the end game builds try to stack as much defense as possible, and CJ 3% defense are often very useful for this matter.
Of course you can build a scrapper with Fly without a problem. Air Superiority is a very nice attack to have while leveling btw 
FYI, Hover offers some defense as Combat Jumping. The trade off is your movement will be slower and the endurance cost is double. I run Hover/Fly on several of my scrappers, including my DM/DA. Every travel power has it's pros and cons, I recommend choosing what fits your character concept best.
I should clarify, my DM/DA actually has Hover and Combat Jumping.
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Yes you can take any travel power you want too. They are all good and all bring different things to builds.
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Wow. Thanks for all the quick and friendly responses. Its kind of shocking!
I'll stop worrying a bit now!
I have two level 50 scrappers with Fly (and Air Superiority, it's a very fun attack!), and two level 50s with teleport
Worry not, your scrapper will manage to kick immense amounts of butt no matter the travel power you choose!
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I take flight on nearly all my scrappers (and tanks and controllers...) and spend most of my time solo. It works just fine.
I have both Hover and Combat Jumping on my Kat/Fire as well, and Super Jump and Fly...
I took it on my martial arts guy so I could come in with flying crane kicks. Oh ya picture it's as fun to use as it is funny to watch.
Almost every toon I make, no matter what AT it is has fly as it's first travel power. Not so much because I like flight, but because I like Air Superiority. With a few recharge enhancements it can permanently knockdown a target, which is very handy in the early to middle levels when you don't have much defenses built up to handle the occasional boss spawn.
Hover is a little annoying as a melee toon because it doesn't move very fast at low levels and your do have to move around from target to target during combat. It used to be true that using the autofollow command while flying (I have it bound to F but I don't know if that's the origional key-bind) would stop just outside of melee range. I don't know if that's true anymore now that they've extended the melee range from 5ft to 7ft. But they also made it much less handy to be hovering as a melee toon... but not unplayable nor weaker.
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My DM/Sr has fly, stems back to when defence was broken and AS was great Damage Mitigation but it really is fairly useful still
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I have a Claws/Regen scrapper who has fly and hover, aptly named Flyin Lion. Pretty much solo'd him through the whole game. No worries at all. Play what you want, but make sure you want what you play.
Pardon me if this is a silly question, but I'm new to the game and after looking over the forums for a while it seems like nearly every scrapper takes Combat Jumping and Super Jumping as their travel powers.
Is it even viable to have a scrapper who can fly or would I be seriously impacting my ability to solo by choosing flight?
Thanks in advance!