Reputation is definitely an important factor in getting funded. This isn't just true of Hive proposals, it's true of just about everything in life.
But I don't think this indicates a problem, as long as the person's reputation is deserved. Theoretically, a reputation should be strongly correlated with past performance, and maintenance of that reputation includes continuing to meet expectations, so it's generally only logical to fund people with good reputations, assuming their proposals also make sense.
Now, where this can break down is when someone's reputation doesn't accurately reflect reality. Unfortunately, this does happen more often than is desirable, generally through a process of rampant self-promotion, false claims, shilling, etc to create false reputations. This mostly happens when you don't get a chance to personally interact with the person involved (or at least, not an interaction where the reputational characteristic is observable), so that your knowledge of that person is mostly second-hand, and therefore more difficult to judge.
And this can lead to serious harm, as history has shown us, when people blindly follow someone who's supposed to be a great leader or some kind of special genius, but actually only possesses a complete lack of morals and can lie about their abilities without any compunction (and have others lie for them as well).
Because of the problems with our current methods of determining the correct "reputation" for people, one of my main goals is to enhance Hive so that it can allow for better "computation" of someone's abilities in various areas (e.g. various forms of reputation). After we get through our initial optimization of Hive, this is where I plan to spend a lot of my time.
Also, as an aside, I can say that it's not so simple as "founders get funded". For example, in BitShares, which was the precursor chain to Hive, the founder of that chain wasn't able to get funded for a number of proposals he made for that chain's worker proposal system. And arguably, that's one of the reasons he stopped working on that chain and started Steem. Now there were definitely reasons why he didn't get funded (he made a bunch of mistakes that had damaged his reputation), but it does show that being at the beginning isn't always enough.