My son played for a very competitive, but very affordable travel team. It was made up of generally blue collar families, and every player on that team played in college. He was lucky because they played in SoCal and had high level competition in the Arizona/SoCal region and did not have to travel very far. He told me the other day that this really prepared him for both HS and college ball as he had faced high level competition growing up which gave him confidence against any player. He also played in a couple of "pick up" PG teams when his travel team did not go to a PG event. So there are ways to get it done cost effectively, but you have to work at it.
I realize this is more difficult outside of hotbed baseball areas, but with research and work it can be done. Unless you are a blue chip player just thinking that you just need to be on a team is a huge mistake. You have to do your homework, and know what level your son can compete at, and be in contact with those schools and let them know you will be a "X" event, the team and your schedule. Don't waste your time (or the coaches) trying to get on a top 50 RPI college team if you are not that level of player.
Regarding the D3 discussion, PG is correct, in the D3 world there is a huge variation in levels of baseball. My son's national championship D3 team had 6 pitchers throwing in the 90's. (BTW they had a lefty who was very effective at 82) When they played a top 50 RPI D1 team their pitchers were generally sitting 95, and we were generally sitting 91. Within his D3 league there were a couple of teams that could not consistently beat a good HS team IMO.
If I had to do it again, I would focus more on training, skills, strength and conditioning, and a little less travel, but travel ball is a must IMO if you are going to play in college at a high level.