Talk about asking the tough questions...
I'd say there are a number of factors that causesome folks to be less enthusiastic about fantasy baseball late in the season than in April. You're certainly right that fantasy football season plays a role - this is the old toy vs. new toy effect. And all the problems facing baseball, from steroids to labor disputes, doesn't help.
Also, the pecking order in most leagues will be pretty much decided by now. Unfortunately, in many more casual leagues, this means that the teams at the bottom of the standings may go inactive, which detracts from the overall fun. Trading deadlines are in the past, which takes away an element that many find especially entertaining.
I suppose it really depends on where you are in the standings. If you're in 7th place, 7 points out of 6th and 5 above 8th, there's not much left to fight for. If you're in a tight pennant race, this can be the most exciting time of the year. In my primary keeper league, for instance, I've just managed to claw my way back from a 6-point September deficit to a two point lead, and now have to toe the line between fighting to stay in first and still adding a potential keeper or two next year. In this league, I've never been more involved than I am now, football season or not.
There are several ways to counter late-season malaise. One is to use roto or head-to-head formats instead of straight points. In head-to-head, bragging rights are at stake every single week, while in roto, there's always a way to try and make up a few points, even if it means benching Sammy Sosa in favor of Dave Roberts to get a few extra steals. Another is to go with a keeper format. With September call-ups now available, there are a lot of interesting things happening in keeper leagues right about now. And the most important thing is probably to play with a group of people who will remain active owners all season.
At any rate, fantasy baseball will never be as bright and shiny in September as it was in April, but it doesn't necessarily have to get old.
Now if only we could do something about steroids, too...