You get used to it. The reason 「は」 in 「私は」/「わたしは」 is used is because that is how the topic marking particle is written. There are other particles this applies to as well. You just need to learn and accept them.
The only particles this happens with are "wa" は, "e" へ, and "o" を. I'm pretty sure it stems from archaic spelling rules which have been simplified over time. At any rate, if you know those three, you won't have a problem with anything else.
High time to finish what I've started. || Anki vocabulary drive: 5,000/10k. Restart coming soon. || Dig my Road to Katakana tutorial on the App store.
Yeah, Psy is right. Those are the only 3 and they do stem from old spelling rules. They used to be pronounced that way, but over times sounds and spellings changed, but the old ways (for writing grammar) stayed preserved.