Proxies are a "time and a place" thing in TCGs and Minis. Here's my perspective as a former TCG player and current small-scale minis players:
Proxies are great if you've got an idea for a new strategy, but don't want to drop money on eBay for a specific piece until you've made sure that said strategy has a sound premise. My former roommate and I spent many afternoons testing wild ideas in various games using proxies.
They're also great if you show up at your buddy's house and left one of your rares sitting out on your table at home. It's casual, everyone knows you have that piece, and the aim is to just mess around a bit.
However,
I would NEVER attempt to use a proxy in a DCI-sanctioned event or at a local gaming hall/gaming club where I might be playing with people I'm not friends with or don't know at all. DCI bans proxies even at casual events, and people are serious about keeping their events DCI compliant because of the national rankings and periodic prize kits/pre-release bonuses/goodies that come with being in good standing. Judges and other players are pretty serious about the proxy rule; not because they're trying to be dicks, but because they're directly responsible for maintaining the compliance and reputation of their events.
Beyond that, many TCG/minis games (and some local gaming stores too) are perpetually one or two sets away from being canceled. When you're aware of the fact that your hobby (or local store) could get the axe at anytime, you don't foster a culture of not buying pieces or boosters.
Finally, for a lot of the guys that can only afford one booster or eBay purchase a paycheck, trading is half the fun. The encouragement of proxies kills the thrill of haggling for that piece you need, or wheeling and dealing for the best offer to take the piece you don't need off your hands.
I completely understand why you'd be confused by the reaction to proxies/homemades; I was too when I first started playing TCGs/Minis. On the other hand, widespread proxy play back in '95 ended up being a major player in killing off my interest in Magic, and I've seen a few of the minis games I play dropped from my local gaming store due to low sales.